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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_A5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922162 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144356,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989131 | GSM922162 | GSE36552 | 0.728284 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144356 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989131 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_A6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922163 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144357,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989132 | GSM922163 | GSE36552 | 0.772416 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144357 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989132 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_A7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922164 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144358,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989133 | GSM922164 | GSE36552 | 0.504994 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144358 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989133 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_A8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922165 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144359,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989134 | GSM922165 | GSE36552 | 0.474868 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144359 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989134 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_E1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922166 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144360,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989135 | GSM922166 | GSE36552 | 0.518651 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144360 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989135 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_E2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922167 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144361,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989136 | GSM922167 | GSE36552 | 0.506802 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144361 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989136 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_E3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922168 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144362,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989137 | GSM922168 | GSE36552 | 0.20913 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144362 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989137 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_E4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922169 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144363,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989138 | GSM922169 | GSE36552 | 0.269811 | 8-cell embryo#2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#2 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144363 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989138 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922170 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144364,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989139 | GSM922170 | GSE36552 | 0.241184 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144364 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989139 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922171 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144365,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989140 | GSM922171 | GSE36552 | 0.303824 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144365 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989140 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922172 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144366,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989141 | GSM922172 | GSE36552 | 0.784399 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144366 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989141 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922173 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144367,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989142 | GSM922173 | GSE36552 | 0.587705 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144367 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989142 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922174 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144368,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989143 | GSM922174 | GSE36552 | 0.558261 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144368 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989143 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922175 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144369,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989144 | GSM922175 | GSE36552 | 0.595962 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144369 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989144 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922176 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144370,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989145 | GSM922176 | GSE36552 | 0.803142 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144370 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989145 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_K8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922177 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144371,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989146 | GSM922177 | GSE36552 | 0.718147 | 8-cell embryo#3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | 8-cell embryo#3 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144371 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989146 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922178 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144372,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989147 | GSM922178 | GSE36552 | 0.502895 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144372 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989147 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922179 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144373,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989148 | GSM922179 | GSE36552 | 0.586907 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144373 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989148 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922180 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144374,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989149 | GSM922180 | GSE36552 | 0.526798 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144374 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989149 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922181 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144375,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989150 | GSM922181 | GSE36552 | 0.264802 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144375 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989150 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922182 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144376,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989151 | GSM922182 | GSE36552 | 0.39149 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144376 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989151 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922183 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144377,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989152 | GSM922183 | GSE36552 | 0.320165 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144377 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989152 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922184 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144378,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989153 | GSM922184 | GSE36552 | 0.802827 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144378 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989153 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_D8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922185 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144379,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989154 | GSM922185 | GSE36552 | 0.619692 | Morulae #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #1 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144379 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989154 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922186 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144380,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989155 | GSM922186 | GSE36552 | 0.65969 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144380 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989155 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922187 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144381,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989156 | GSM922187 | GSE36552 | 0.499106 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144381 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989156 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922188 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144382,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989157 | GSM922188 | GSE36552 | 0.599373 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144382 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989157 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922189 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144383,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989158 | GSM922189 | GSE36552 | 0.557857 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144383 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989158 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922190 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144384,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989159 | GSM922190 | GSE36552 | 0.637209 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144384 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989159 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922191 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144385,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989160 | GSM922191 | GSE36552 | 0.611765 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144385 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989160 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922192 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144386,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989161 | GSM922192 | GSE36552 | 0.301243 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144386 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989161 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_F8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922193 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144387,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989162 | GSM922193 | GSE36552 | 0.694687 | Morulae #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Morulae #2 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144387 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989162 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922194 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144388,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989163 | GSM922194 | GSE36552 | 0.757325 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144388 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989163 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922195 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144389,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989164 | GSM922195 | GSE36552 | 0.735755 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144389 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989164 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922196 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144390,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989165 | GSM922196 | GSE36552 | 0.446179 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144390 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989165 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922197 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144391,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989166 | GSM922197 | GSE36552 | 0.58167 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144391 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989166 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922198 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144392,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989167 | GSM922198 | GSE36552 | 0.592258 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144392 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989167 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922199 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144393,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989168 | GSM922199 | GSE36552 | 0.941874 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144393 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989168 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922200 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144394,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989169 | GSM922200 | GSE36552 | 0.902324 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144394 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989169 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G9.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922201 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144395,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989170 | GSM922201 | GSE36552 | 0.559396 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144395 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989170 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G10.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922202 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144396,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989171 | GSM922202 | GSE36552 | 0.616505 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144396 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989171 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G11.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922203 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144397,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989172 | GSM922203 | GSE36552 | 0.851241 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#10 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144397 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989172 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G12.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922204 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144398,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989173 | GSM922204 | GSE36552 | 0.534356 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#11 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144398 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989173 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_G13.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922205 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144399,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989174 | GSM922205 | GSE36552 | 0.711282 | Late blastocyst #1 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #1 -Cell#12 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144399 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989174 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922206 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144400,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989175 | GSM922206 | GSE36552 | 0.695331 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144400 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989175 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922207 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144401,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989176 | GSM922207 | GSE36552 | 0.66741 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144401 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989176 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922208 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144402,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989177 | GSM922208 | GSE36552 | 0.779267 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144402 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989177 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922209 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144403,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989178 | GSM922209 | GSE36552 | 0.674325 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144403 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989178 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922210 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144404,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989179 | GSM922210 | GSE36552 | 0.747228 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144404 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989179 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922211 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144405,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989180 | GSM922211 | GSE36552 | 0.647676 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144405 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989180 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922212 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144406,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989181 | GSM922212 | GSE36552 | 0.845481 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144406 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989181 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922213 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144407,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989182 | GSM922213 | GSE36552 | 0.564857 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144407 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989182 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H9.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922214 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144408,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989183 | GSM922214 | GSE36552 | 0.588744 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144408 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989183 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_H10.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922215 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144409,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989184 | GSM922215 | GSE36552 | 0.620537 | Late blastocyst #2 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #2 -Cell#10 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144409 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989184 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922216 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144410,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989185 | GSM922216 | GSE36552 | 0.68766 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144410 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989185 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922217 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144411,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989186 | GSM922217 | GSE36552 | 0.717223 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144411 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989186 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922218 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144412,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989187 | GSM922218 | GSE36552 | 0.556127 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144412 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989187 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922219 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144413,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989188 | GSM922219 | GSE36552 | 0.67558 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144413 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989188 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922220 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144414,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989189 | GSM922220 | GSE36552 | 0.735999 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144414 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989189 |
|
1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922221 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144415,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989190 | GSM922221 | GSE36552 | 0.773951 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144415 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989190 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922222 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144416,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989191 | GSM922222 | GSE36552 | 0.783534 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144416 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989191 |
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1 | cell type: human preimplantation blastomere,developmental stage: early blastomere,tissue: human preimplantation embryos | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_R8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922223 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144417,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989192 | GSM922223 | GSE36552 | 0.501755 | Late blastocyst #3 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | Late blastocyst #3 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144417 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989192 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922224 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144418,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989193 | GSM922224 | GSE36552 | 0.526208 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144418 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989193 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922225 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144419,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989194 | GSM922225 | GSE36552 | 0.445646 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144419 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989194 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922226 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144420,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989195 | GSM922226 | GSE36552 | 0.638154 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144420 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989195 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922227 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144421,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989196 | GSM922227 | GSE36552 | 0.45626 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#7 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144421 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989196 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922228 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144422,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989197 | GSM922228 | GSE36552 | 0.424543 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144422 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989197 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_M10.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922230 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144424,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989199 | GSM922230 | GSE36552 | 0.476832 | hESC passage#0 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#0 -Cell#10 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144424 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989199 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922250 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144444,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989219 | GSM922250 | GSE36552 | 0.799423 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144444 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989219 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922251 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144445,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989220 | GSM922251 | GSE36552 | 0.684134 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144445 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989220 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P5.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922252 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144446,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989221 | GSM922252 | GSE36552 | 0.838045 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144446 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989221 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922253 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144447,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989222 | GSM922253 | GSE36552 | 0.328417 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#4 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144447 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989222 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P9.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922254 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144448,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989223 | GSM922254 | GSE36552 | 0.455914 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#5 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144448 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989223 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P11.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922255 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144449,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989224 | GSM922255 | GSE36552 | 0.647552 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#6 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144449 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989224 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P13.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922257 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144451,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989226 | GSM922257 | GSE36552 | 0.545512 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#8 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144451 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989226 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P14.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922258 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144452,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989227 | GSM922258 | GSE36552 | 0.749064 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144452 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989227 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_P15.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922259 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144453,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989228 | GSM922259 | GSE36552 | 0.570583 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#10 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144453 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989228 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S1.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922261 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144455,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989230 | GSM922261 | GSE36552 | 0.349973 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#12 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144455 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989230 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S2.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922262 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144456,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989231 | GSM922262 | GSE36552 | 0.308114 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144456 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989231 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S3.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922263 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144457,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989232 | GSM922263 | GSE36552 | 0.274697 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#14 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144457 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989232 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S4.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922264 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144458,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989233 | GSM922264 | GSE36552 | 0.235904 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#15 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144458 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989233 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S6.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922266 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144460,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989235 | GSM922266 | GSE36552 | 0.331233 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#17 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144460 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989235 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S7.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922267 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144461,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989236 | GSM922267 | GSE36552 | 0.269622 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#18 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144461 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989236 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S8.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922268 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144462,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989237 | GSM922268 | GSE36552 | 0.479558 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#19 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144462 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989237 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S9.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922269 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144463,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989238 | GSM922269 | GSE36552 | 0.320381 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#20 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144463 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989238 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S10.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922270 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144464,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989239 | GSM922270 | GSE36552 | 0.355114 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#21 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144464 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989239 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S11.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922271 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144465,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989240 | GSM922271 | GSE36552 | 0.636822 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#22 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144465 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989240 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S12.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922272 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144466,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989241 | GSM922272 | GSE36552 | 0.557052 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#23 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144466 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989241 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S13.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922273 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144467,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989242 | GSM922273 | GSE36552 | 0.498263 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#24 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144467 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989242 |
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1 | cell type: human embryonic stem cell,developmental stage: peri-implantation stem cells,tissue: human embryonic stem cell line | 5 Yiheyuan Road | Beijing | China | Peking University | Mingyu,,Yang | Reads mapping: We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8" [Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60],Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ⥠0.1 as expressed genes in the following analysis,Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842],Merge the *.bed files from samples in the same stage [available on Series records],Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records],Genome_build: hg19,Sample_S14.expression.txt: hg19 | Amplied single cell cDNAs were further amplied for another ten cycles of PCR.Then it was sonicated into 200~500bp fragments ,then the standard TruSeq DNA library preparation kit was used following the manualfactory suggestion protocol | GSM922274 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX144468,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00989243 | GSM922274 | GSE36552 | 0.237602 | hESC passage#10 | Public on Aug 10 2013 | Apr 25 2012 | 9606 | hESC passage#10 -Cell#25 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX144468 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00989243 |
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1 | cell type: ESC,cell line: BG01 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925605 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145383,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990520 | GSM925605 | GSE37686 | 0.355719 | ESC | Public on Aug 01 2012 | May 01 2012 | 9606 | ESC BG01 rep1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145383 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990520 |
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1 | cell type: ESC,cell line: BG01 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925606 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145384,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990521 | GSM925606 | GSE37686 | 0.142944 | ESC | Public on Aug 01 2012 | May 01 2012 | 9606 | ESC BG01 rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145384 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990521 |
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1 | cell type: partially differentiated ESC,parental cell line: BG01 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925607 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145385,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990522 | GSM925607 | GSE37686 | 0.287533 | partially differentiated ESC | Public on Aug 01 2012 | May 01 2012 | 9606 | partially differentiated ESC BG01 partial diff | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145385 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990522 |
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1 | cell type: primary fetal RPE | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925608 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145386,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990523 | GSM925608 | GSE37686 | 0 | fetal RPE | Public on Aug 01 2012 | May 01 2012 | 9606 | fetal RPE | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145386 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990523 |
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1 | cell type: ESC,parental cell line: H9 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925609 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145387,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990524 | GSM925609 | GSE37686 | 0.457691 | ESC | Public on Aug 01 2012 | May 01 2012 | 9606 | ESC H9 ESC | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145387 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990524 |
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1 | cell type: pigmented cluster,parental cell line: H9 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925610 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145388,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990525 | GSM925610 | GSE37686 | 0.109746 | pigmented cluster | Public on Aug 01 2012 | May 01 2012 | 9606 | pigmented cluster H9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145388 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990525 |
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1 | cell type: partial differentiated ESC,parental cell line: H9 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925611 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145389,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990526 | GSM925611 | GSE37686 | 0.201777 | partial differentiated ESC | Public on Aug 01 2012 | May 01 2012 | 9606 | partial differentiated ESC H9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145389 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990526 |
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1 | cell type: ES-RPE,parental cell line: H9 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925612 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145390,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990527 | GSM925612 | GSE37686 | 0.14578 | ES-RPE | Public on Aug 01 2012 | May 01 2012 | 9606 | ES-RPE H9 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145390 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990527 |
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1 | cell type: ES-RPE,parental cell line: hiPS2 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925613 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145391,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990528 | GSM925613 | GSE37686 | 0.019684 | ES-RPE | Public on Aug 01 2012 | May 01 2012 | 9606 | ES-RPE hiPS2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145391 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990528 |
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1 | cell type: ES-RPE,parental cell line: HSF1 | Gonda BLDG Rm. 6554, P.O.Box 957088 | Los Angeles | USA | UCLA | Kevin,,Huang | Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -v1 -a -m 10 --best --strata,Reads Per Megabase of library size (RPM) were calculated by counting the number of reads falling in the miRNA locus and normalizing by the size of the library.,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample | Total RNA (1~10μg) was ligated with a pair of Illumina adaptors to their 5â²and 3â²ends. After reverse transcription, the small RNA molecules were amplified using multiplex adaptor primers for 12 cycles and the fragments around 93~100 bp (small RNA+adaptors) were then isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina's HiSeq2000 sequencing according to the manufacturer's instructions. | GSM925614 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX145392,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN00990529 | GSM925614 | GSE37686 | 0.116137 | ES-RPE | Public on Aug 01 2012 | May 01 2012 | 9606 | ES-RPE HSF1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX145392 | https://www.ncbi.nlm.nih.gov/biosample/SAMN00990529 |