channel_count
int64 1
1
| characteristics_ch1
stringlengths 6
9.77k
| contact_address
stringlengths 1
229
| contact_city
stringlengths 1
47
| contact_country
stringclasses 71
values | contact_institute
stringlengths 2
128
| contact_name
stringlengths 4
74
| contact_zip
stringclasses 1
value | data_processing
stringlengths 4
10.6k
| extract_protocol_ch1
stringlengths 6
14.3k
| geo_accession
stringlengths 9
10
| instrument_model
stringclasses 13
values | last_update_date
stringlengths 11
11
| library_selection
stringclasses 6
values | library_source
stringclasses 5
values | library_strategy
stringclasses 1
value | molecule_ch1
stringclasses 7
values | organism_ch1
stringclasses 1
value | platform_id
stringclasses 13
values | relation
stringlengths 0
2.61k
| sample
stringlengths 9
10
| series_id
stringlengths 8
29
| singlecellprobability
float64 0
1
| source_name_ch1
stringlengths 1
253
| status
stringlengths 21
21
| submission_date
stringlengths 11
11
| taxid_ch1
stringclasses 1
value | title
stringlengths 1
120
| type
stringclasses 1
value | sra
stringlengths 47
49
⌀ | biosample
stringlengths 51
51
⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | labexpid: 12515,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087856 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245434,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924693 | GSM1087856 | GSE44618 | 0.099405 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12515-100mers-GM12878_100A-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245434 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924693 |
|
1 | labexpid: 12516,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087857 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245435,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924694 | GSM1087857 | GSE44618 | 0.051084 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12516-100mers-GM12878_100B-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245435 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924694 |
|
1 | labexpid: 12517,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087858 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245436,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924695 | GSM1087858 | GSE44618 | 0.027726 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12517-100mers-GM12878_30A-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245436 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924695 |
|
1 | labexpid: 12518,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087859 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245437,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924696 | GSM1087859 | GSE44618 | 0.096423 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12518-100mers-GM12878_30B-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245437 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924696 |
|
1 | labexpid: 12519,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087860 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245438,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924697 | GSM1087860 | GSE44618 | 0.32223 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12519-100mers-GM12878_10A_12-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245438 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924697 |
|
1 | labexpid: 12520,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087861 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245439,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924698 | GSM1087861 | GSE44618 | 0.177186 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12520-100mers-GM12878_10B_10-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245439 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924698 |
|
1 | labexpid: 12522,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087862 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245440,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924699 | GSM1087862 | GSE44618 | 0.437191 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12522-100mers-GM12878_183-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245440 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924699 |
|
1 | labexpid: 12523,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087863 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245441,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924700 | GSM1087863 | GSE44618 | 0.487559 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12523-100mers-GM12878_184-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245441 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924700 |
|
1 | labexpid: 12536,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087867 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245445,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924704 | GSM1087867 | GSE44618 | 0.63624 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12536-100mers-GM12878_188-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245445 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924704 |
|
1 | labexpid: 12537,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087868 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245446,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924705 | GSM1087868 | GSE44618 | 0.512173 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12537-100mers-GM12878_189-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245446 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924705 |
|
1 | labexpid: 12538,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087869 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245447,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924706 | GSM1087869 | GSE44618 | 0.739706 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12538-100mers-GM12878_190-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245447 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924706 |
|
1 | labexpid: 12539,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087870 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245448,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924707 | GSM1087870 | GSE44618 | 0.506757 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12539-100mers-GM12878_191-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245448 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924707 |
|
1 | labexpid: 12542,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087873 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245451,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924710 | GSM1087873 | GSE44618 | 0.384293 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12542-100mers-GM12878_194-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245451 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924710 |
|
1 | labexpid: 12543,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087874 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245452,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924711 | GSM1087874 | GSE44618 | 0.368249 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12543-100mers-GM12878_195-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245452 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924711 |
|
1 | labexpid: 12818,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087875 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245453,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924712 | GSM1087875 | GSE44618 | 0.501578 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12818-100mers-GM12878_200-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245453 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924712 |
|
1 | labexpid: 12819,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087876 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245454,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924713 | GSM1087876 | GSE44618 | 0.56044 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 12819-100mers-GM12878_205-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245454 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924713 |
|
1 | labexpid: 13275,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087879 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245457,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924716 | GSM1087879 | GSE44618 | 0.21076 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13275-100mers-GM12878-10ng_2-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245457 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924716 |
|
1 | labexpid: 13279,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087883 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245461,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924720 | GSM1087883 | GSE44618 | 0.952836 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13279-100mers-GM12878-207-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245461 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924720 |
|
1 | labexpid: 13282,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087884 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78311,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245462,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924721 | GSM1087884 | GSE44618 | 0.413075 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13282-100mers-GM12878-235-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78311) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245462 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924721 |
|
1 | labexpid: 13283,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087885 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78308,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245463,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924722 | GSM1087885 | GSE44618 | 0.458701 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13283-100mers-GM12878-236-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78308) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245463 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924722 |
|
1 | labexpid: 13285,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087887 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78307,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245465,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924724 | GSM1087887 | GSE44618 | 0.297674 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13285-100mers-GM12878-238-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78307) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245465 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924724 |
|
1 | labexpid: 13286,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087888 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78310,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245466,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924725 | GSM1087888 | GSE44618 | 0.494188 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13286-100mers-GM12878-239-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78310) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245466 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924725 |
|
1 | labexpid: 13287,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087889 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78312,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245467,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924726 | GSM1087889 | GSE44618 | 0.761146 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13287-100mers-GM12878-240-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78312) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245467 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924726 |
|
1 | labexpid: 13288,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087890 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78309,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245468,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924727 | GSM1087890 | GSE44618 | 0.541279 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13288-100mers-GM12878-242-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78309) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245468 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924727 |
|
1 | labexpid: 13289,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087891 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78339,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245469,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924728 | GSM1087891 | GSE44618 | 0.71712 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13289-100mers-GM12878-243-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78339) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245469 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924728 |
|
1 | labexpid: 13290,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087892 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78451,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245470,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924729 | GSM1087892 | GSE44618 | 0.49643 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13290-100mers-GM12878-244-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78451) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245470 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924729 |
|
1 | labexpid: 13291,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087893 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | Superseded by: GSE78421,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245471,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924730 | GSM1087893 | GSE44618 | 0.4552 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13291-100mers-GM12878-245-TopHat-1.4.1-GENCODE-V13 (superseded by GSE78421) | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245471 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924730 |
|
1 | cell line: GM12878,labexpid: 13300 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087894 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245472,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924731 | GSM1087894 | GSE44618 | 0.746542 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13300-100mers-GM12878-254_10cells-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245472 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924731 |
|
1 | labexpid: 13301,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087895 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245473,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924732 | GSM1087895 | GSE44618 | 0.442634 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13301-100mers-GM12878-255_11cells-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245473 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924732 |
|
1 | labexpid: 13302,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087896 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245474,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924733 | GSM1087896 | GSE44618 | 0.515367 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13302-100mers-GM12878-256_100cells-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245474 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924733 |
|
1 | labexpid: 13303,cell line: GM12878 | 1200 E California Blvd M/C 156-29 | Pasadena | USA | California Institute of Technology | Diane,E,Trout | Libraries were pooled and sequenced on the Illumina HiSeq or GAIIx. Single-end reads of 100bp length were obtained (excluding the barcode sequence). Sequencing reads were demultiplexed based on barcode sequences and aligned against the male or female hg19 version of the human genome (depending on the sex of the cell line or donor) with TopHat 1.4.1 and the GENCODE V13 annotation using the --GTF option and with de novo junction discovery turned on. Only the first read was used for the few libraries that were sequenced as paired end. | Single GM12878 cells were picked from a culture dish using a micropipet. They were deposited into cell lysis solution (Clontech SMARTer Ultra Low RNA kit) and frozen at -80C. Amplified cDNA was then prepared following the manufacturer's protocol. The amplified cDNA was fragmented and tagged using the Nextera Illumina Genomic DNA prep kit, according to the manufacturer's protocol. The fragmented cDNA libraries were then sequenced on the Illumina HiSeq 2000 instrument. | GSM1087897 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245475,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924734 | GSM1087897 | GSE44618 | 0.19425 | GM12878 | Public on Nov 21 2013 | Feb 25 2013 | 9606 | 13303-100mers-GM12878-257_100cells-TopHat-1.4.1-GENCODE-V13 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245475 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924734 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088200 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245575,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924861 | GSM1088200 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M7_naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245575 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924861 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088204 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245579,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924865 | GSM1088204 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245579 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924865 |
|
1 | status: healthy,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088205 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245580,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924866 | GSM1088205 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M29_naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245580 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924866 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088206 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245581,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924867 | GSM1088206 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M7_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245581 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924867 |
|
1 | status: healthy,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088207 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245582,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924868 | GSM1088207 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M8_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245582 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924868 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088210 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245585,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924871 | GSM1088210 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245585 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924871 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088211 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245586,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924872 | GSM1088211 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M26_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245586 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924872 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088212 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245587,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924873 | GSM1088212 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M27_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245587 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924873 |
|
1 | status: healthy,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088213 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245588,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924874 | GSM1088213 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M30_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245588 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924874 |
|
1 | status: healthy,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088214 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245589,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924875 | GSM1088214 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M7_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245589 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924875 |
|
1 | status: healthy,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088218 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245593,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924879 | GSM1088218 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245593 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924879 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088219 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245594,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924880 | GSM1088219 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M26_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245594 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924880 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088220 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245595,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924881 | GSM1088220 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M27_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245595 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924881 |
|
1 | status: healthy,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088225 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245600,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924886 | GSM1088225 | GSE44639 | 0.261906 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M9_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245600 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924886 |
|
1 | status: healthy,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088227 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245602,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924888 | GSM1088227 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245602 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924888 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088230 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245605,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924891 | GSM1088230 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M9_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245605 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924891 |
|
1 | status: healthy,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088231 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245606,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924892 | GSM1088231 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M10_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245606 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924892 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088232 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245607,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924893 | GSM1088232 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245607 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924893 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088233 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245608,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924894 | GSM1088233 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M7_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245608 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924894 |
|
1 | status: healthy,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088234 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245609,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924895 | GSM1088234 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M8_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245609 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924895 |
|
1 | status: healthy,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088235 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245610,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924896 | GSM1088235 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M9_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245610 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924896 |
|
1 | status: healthy,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088236 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245611,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924897 | GSM1088236 | GSE44639 | 0.432695 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M10_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245611 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924897 |
|
1 | status: healthy,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088237 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245612,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924898 | GSM1088237 | GSE44639 | 0.261906 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | M12_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245612 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924898 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088238 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245613,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924899 | GSM1088238 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245613 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924899 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088239 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245614,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924900 | GSM1088239 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P2_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245614 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924900 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088240 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245615,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924901 | GSM1088240 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P3_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245615 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924901 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088242 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245617,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924903 | GSM1088242 | GSE44639 | 0.261906 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P5_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245617 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924903 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088243 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245618,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924904 | GSM1088243 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P6_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245618 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924904 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088244 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245619,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924905 | GSM1088244 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_Naive | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245619 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924905 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088245 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245620,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924906 | GSM1088245 | GSE44639 | 0.261906 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245620 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924906 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088248 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245623,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924909 | GSM1088248 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P4_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245623 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924909 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088249 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245624,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924910 | GSM1088249 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P5_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245624 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924910 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088250 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245625,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924911 | GSM1088250 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P6_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245625 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924911 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088251 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245626,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924912 | GSM1088251 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_rTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245626 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924912 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088252 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245627,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924913 | GSM1088252 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245627 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924913 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088253 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245628,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924914 | GSM1088253 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P2_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245628 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924914 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088254 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245629,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924915 | GSM1088254 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P3_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245629 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924915 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088255 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245630,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924916 | GSM1088255 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P4_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245630 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924916 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088256 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245631,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924917 | GSM1088256 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P5_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245631 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924917 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088257 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245632,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924918 | GSM1088257 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P6_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245632 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924918 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088258 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245633,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924919 | GSM1088258 | GSE44639 | 0.365506 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_aTreg | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245633 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924919 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088259 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245634,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924920 | GSM1088259 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245634 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924920 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088260 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245635,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924921 | GSM1088260 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P2_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245635 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924921 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088261 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245636,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924922 | GSM1088261 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P3_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245636 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924922 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088262 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245637,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924923 | GSM1088262 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P4_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245637 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924923 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088263 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245638,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924924 | GSM1088263 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P5_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245638 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924924 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088265 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245640,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924926 | GSM1088265 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_Tcm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245640 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924926 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088266 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245641,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924927 | GSM1088266 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245641 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924927 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088267 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245642,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924928 | GSM1088267 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P2_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245642 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924928 |
|
1 | status: pre-T1D,barcode: CATTGTTAGC | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088268 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245643,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924929 | GSM1088268 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P3_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245643 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924929 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088270 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245645,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924931 | GSM1088270 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P5_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245645 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924931 |
|
1 | status: pre-T1D,barcode: GTGCATCCTA | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088271 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245646,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924932 | GSM1088271 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P6_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245646 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924932 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088272 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245647,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924933 | GSM1088272 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_Tem | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245647 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924933 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088273 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245648,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924934 | GSM1088273 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P1_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245648 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924934 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088275 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245650,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924936 | GSM1088275 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P3_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245650 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924936 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088276 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245651,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924937 | GSM1088276 | GSE44639 | 0.369613 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P4_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245651 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924937 |
|
1 | status: pre-T1D,barcode: TCAACGGTAG | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088278 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245653,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924939 | GSM1088278 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P6_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245653 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924939 |
|
1 | status: pre-T1D,barcode: AGCCTAAGCT | 9 Princes Street | Fitzroy | Australia | St Vincent's Institute of Medical Research | Mark,,Chong | Base calling,Barcode deconvolution and stripping,Alignment to mature miRNA database (miRBase),Alignment of remaining reads to miRNA precursor database (miRBase),Read abundance counting and normalization to library read size,Genome_build: miRBase 17,Supplementary_files_format_and_content: Excel spread sheet: miRNA identity and count | Total RNA was extracted from sorted CD4+ T cell subsets with TRI Reagent (Ambion) following the manufacturerâs protocol with one modification: RNA was precipitated with ethanol at -80°C (instead of isopropanol on ice) in order to obtain all RNAs including miRNAs.,Small RNA libraries were constructed for sequencing on Illumina GAII/HiSeq platforms, essentially as described previously (18; 29), but with addition of barcoding. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5â end of each library. | GSM1088279 | Illumina HiSeq 2000 | May 15 2019 | size fractionation | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245654,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924940 | GSM1088279 | GSE44639 | 0.3539 | CD4+ T cells | Public on Dec 31 2015 | Feb 25 2013 | 9606 | P7_Ttm | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245654 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924940 |
|
1 | cell type: hiPSCs,passages: 10,clone: 7 | Number 9, Se Yuan Road | Nantong | China | Nantong University | Gangcai,,Xie | Image files were preprocessed by illumina software, which generates qseq files,qseq files were converted into fastq files by ruby scripts, and only the ones passing illumina quality controls were retained,Reads were mapped onto human reference genome hg19 by Tophat-1.3.0,Counts on Gencode Genes and RepeatMasker annotated repeat elements were calculated,Differentially expressed repeat elements were calculated by ruby scripts,Genome_build: hg19 | Total RNA was extracted from embryoid bodies using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using TURBO DNA-free⢠Kit (Ambion) and a second RNA extraction with TRIzol was performed.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols | GSM1088317 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245555,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924849 | GSM1088317 | GSE44646,GSE54726 | 0.127812 | iPS | Public on Oct 09 2014 | Feb 25 2013 | 9606 | iPS | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245555 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924849 |
|
1 | tissue: hiPSC-derived embryoid bodies,passages: 10,clone: 7 | Number 9, Se Yuan Road | Nantong | China | Nantong University | Gangcai,,Xie | Image files were preprocessed by illumina software, which generates qseq files,qseq files were converted into fastq files by ruby scripts, and only the ones passing illumina quality controls were retained,Reads were mapped onto human reference genome hg19 by Tophat-1.3.0,Counts on Gencode Genes and RepeatMasker annotated repeat elements were calculated,Differentially expressed repeat elements were calculated by ruby scripts,Genome_build: hg19 | Total RNA was extracted from embryoid bodies using TRIzol (Invitrogen) following the manufacturer instructions. After extraction a DNAse treatment was applied using TURBO DNA-free⢠Kit (Ambion) and a second RNA extraction with TRIzol was performed.,RNA libraries were prepared for sequencing using Illumina TruSeq protocols | GSM1088319 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245557,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924851 | GSM1088319 | GSE44646,GSE54726 | 0.167091 | EB | Public on Oct 09 2014 | Feb 25 2013 | 9606 | EB | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX245557 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01924851 |
|
1 | donor: C36,genotype/variation: Untreated control | 2347 CIEMAS, 101 Science Drive | Durham | USA | Duke University | Timothy,E,Reddy | Base-calling was performed on instrument using CASAVA software,Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.8 and allowing up to 2 kb between paired reads.,Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by usiong a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).,P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995),Genome_build: hg19,Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript. | Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).,First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000. | GSM1089282 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX246007,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01931869 | GSM1089282 | GSE44718 | 0.003143 | Bronchial Epithelial Cells | Public on May 07 2013 | Feb 27 2013 | 9606 | C36_WT | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX246007 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01931869 |
|
1 | donor: C44,genotype/variation: H2B-GFP-Expressing | 2347 CIEMAS, 101 Science Drive | Durham | USA | Duke University | Timothy,E,Reddy | Base-calling was performed on instrument using CASAVA software,Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.8 and allowing up to 2 kb between paired reads.,Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by usiong a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).,P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995),Genome_build: hg19,Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript. | Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).,First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000. | GSM1089285 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX246010,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01931872 | GSM1089285 | GSE44718 | 0.003143 | Bronchial Epithelial Cells | Public on May 07 2013 | Feb 27 2013 | 9606 | C44_Ctl | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX246010 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01931872 |
|
1 | donor: C29,genotype/variation: DN-GRHL2-Expressing | 2347 CIEMAS, 101 Science Drive | Durham | USA | Duke University | Timothy,E,Reddy | Base-calling was performed on instrument using CASAVA software,Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.8 and allowing up to 2 kb between paired reads.,Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by usiong a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).,P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995),Genome_build: hg19,Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript. | Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).,First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000. | GSM1089286 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX246011,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01931873 | GSM1089286 | GSE44718 | 0.005288 | Bronchial Epithelial Cells | Public on May 07 2013 | Feb 27 2013 | 9606 | C29_DN | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX246011 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01931873 |
|
1 | donor: C44,genotype/variation: DN-GRHL2-Expressing | 2347 CIEMAS, 101 Science Drive | Durham | USA | Duke University | Timothy,E,Reddy | Base-calling was performed on instrument using CASAVA software,Reads were aligned to known RefSeq transcripts from hg19 using Bowtie version 0.12.8 and allowing up to 2 kb between paired reads.,Read counts were normalized and differential expression was called using Deseq (v. 1.10.1) by usiong a chi-squared test to compare fits to a model that contained donor and count (i.e. count ~ donor + condition) to a model that only contained donor information (i.e. count ~ donor).,P-values were converted to a False Discovery Rate using the method of Benjamini and Hochberg (1995),Genome_build: hg19,Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript. | Between 0.5-1 million cells were trypsinized, washed with PBS, pelleted and snap frozen. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was isolated using the Dynabeads mRNA Direct Kit (Invitrogen).,First strand cDNA was generated using SuperScript Vilo cDNA synthesis master mix (Invitrogen), and second strand cDNA was synthesized using E. coli DNA Polymerase I (New England Biolabs) with random hexamer primers. Double stranded cDNA was purified using 1.8X Agentcourt SPRI beads (Beckman Coulter). Double stranded cDNA was fragmented and sequencing adaptors added using Nextera transposase (Illumina) and indexed for sequencing by PCR as described previously. Samples were pooled in equimolar ratios and sequenced on an Illumina HiSeq 2000. | GSM1089288 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX246013,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01931875 | GSM1089288 | GSE44718 | 0.003143 | Bronchial Epithelial Cells | Public on May 07 2013 | Feb 27 2013 | 9606 | C44_DN | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX246013 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01931875 |
|
1 | cell type: renal | No.7 PengFei road | Shenzhen | China | Agricultural Genomes Institute at Shenzhen | Desheng,,Gong | Illumina BclConverter-1.9.0 software used for basecalling.,Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of RNA sequencing reads were aligned to the reference genome (UCSC hg19) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,genome build: hg19,processed data files format and content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample | Total RNA was isolated from 786-O and OS-RC-2 cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5â² phosphatase and 3â² hydroxyls, and adapters were ligated for paired-end sequencing on an Illumina HiSeq 2000. | GSM1093060 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248482,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974780 | GSM1093060 | GSE44866 | 0.008491 | 786-O-RNA-seq | Public on Feb 19 2014 | Mar 05 2013 | 9606 | 786-O-RNA-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248482 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974780 |
|
1 | cell type: renal | No.7 PengFei road | Shenzhen | China | Agricultural Genomes Institute at Shenzhen | Desheng,,Gong | Illumina BclConverter-1.9.0 software used for basecalling.,Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean reads of RNA sequencing reads were aligned to the reference genome (UCSC hg19) using the SOAP aligner with parameters -m 90 -x 500 -l 15 -s 35 -p 4,Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.,genome build: hg19,processed data files format and content: bed files: contained chromsome,reads strart site,reads end sites;tab-delimited text files include RPKM values for each Sample | Total RNA was isolated from 786-O and OS-RC-2 cells using the miRNeasy Kit (Qiagen 74104) according to the manufacturer's protocol. An additional DNaseI digestion step was performed to ensure that the samples were not contaminated with genomic DNA. The RNA purity was assessed using the Agilent bioanalyzer. Total RNA was converted to cDNA using the NuGEN Ovation RNA-Seq System according to the manufacturer's protocol (NuGEN, San Carlos, CA, USA). The cDNA was then used for Illumina sequencing library preparation. DNA fragments were end-repaired to generate blunt ends with 5â² phosphatase and 3â² hydroxyls, and adapters were ligated for paired-end sequencing on an Illumina HiSeq 2000. | GSM1093061 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248483,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974781 | GSM1093061 | GSE44866 | 0.005771 | OS-RC-2-RNA-seq | Public on Feb 19 2014 | Mar 05 2013 | 9606 | OS-RC-2-RNA-seq | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248483 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974781 |
|
1 | cell type: human embryonic stem cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093229 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248484,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974782 | GSM1093229 | GSE44875 | 0.156699 | undifferentiated human ESCs | Public on Jun 01 2014 | Mar 05 2013 | 9606 | ES2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248484 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974782 |
|
1 | cell type: definitive endoderm cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093230 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248485,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974783 | GSM1093230 | GSE44875 | 0.583405 | definitive endoderm cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | DE1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248485 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974783 |
|
1 | cell type: definitive endoderm cells | 82 Walnut St. Unit 3 | Brookline | USA | Harvard Medical School | Yuting,,Liu | All obtained reads from each sample were mapped against the human genome (hg19 build) with Bowtie/Tophat v2.0.2 which allows mapping across splice sites by reads segmentation (Trapnell et al., 2012). All programs were performed with default setting (unless otherwise specified).,The unique mapped reads (69-91% of total reads) were subsequently assembled into transcripts guided by reference annotation (Gencode v14 and Refseq gene models) with Cufflinks v2.0.2 (Trapnell et al., 2012). Expression level of each gene was quantified with normalized FPKM (fragments per kilobase of exon per million mapped fragments).,For the analyses of lncRNAs, cufflinks was used to estimate the transcript level FPKM values with the Gencode v14 lincRNA annotation (Derrien et al., 2012), and human body map lincRNA annotations (Cabili et al., 2011).,processed data file for protein-coding genes:,processed_FPKM_genes_human_pancreatic_lineage_140112.txt,processed data file for lncRNAs:,processed_FPKM_lncRNAs_human_pancreatic_lineage_140112.txt,Genome_build: hg19,Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. | Total RNA was purified from 1,000 sorted cells using ZR RNA microprep kit (Zymo Research, UAS). The cDNA synthesis and amplification was performed with the SMARTer ultra-low input RNA kit (Clontech, US).,The amplified cDNA (10-40 ng) was then fragmented by Covaris S2 sonicator (Covaris, US) and converted to sequencing libraries following the Illuminaâs construction protocol for low input DNA (Illumina, US). Barcoded libraries were pooled and sequenced in Illumina Hiseq 2000 instrument (pair-end 100bp). | GSM1093231 | Illumina HiSeq 2000 | May 15 2019 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL11154 | SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX248486,BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01974784 | GSM1093231 | GSE44875 | 0.557311 | definitive endoderm cells | Public on Jun 01 2014 | Mar 05 2013 | 9606 | DE2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX248486 | https://www.ncbi.nlm.nih.gov/biosample/SAMN01974784 |