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1 | cell line: THP-1,genotype: IRG1 KO,treatment: LPS + IFNg,time: 12Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399942 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537711,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347309 | GSM8399942 | GSE272396 | 0.007642 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, LPS&IFNg Stimulated, 12Hr, rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347309 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537711 |
|
1 | cell line: THP-1,genotype: WT,treatment: Vehicle,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399943 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537710,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347310 | GSM8399943 | GSE272396 | 0.012135 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, Vehicle, 24Hr, rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347310 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537710 |
|
1 | cell line: THP-1,genotype: WT,treatment: LPS + IFNg,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399944 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537709,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347311 | GSM8399944 | GSE272396 | 0.010149 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, LPS&IFNg Stimulated, 24Hr, rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347311 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537709 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: Vehicle,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399945 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537708,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347312 | GSM8399945 | GSE272396 | 0.043236 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, Vehicle, 24Hr, rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347312 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537708 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: LPS + IFNg,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399946 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537707,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347313 | GSM8399946 | GSE272396 | 0.039206 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, LPS&IFNg Stimulated, 24Hr, rep2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347313 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537707 |
|
1 | cell line: THP-1,genotype: WT,treatment: Vehicle,time: 6Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399947 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537706,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347314 | GSM8399947 | GSE272396 | 0.01303 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, Vehicle, 6Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347314 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537706 |
|
1 | cell line: THP-1,genotype: WT,treatment: LPS + IFNg,time: 6Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399948 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537705,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347315 | GSM8399948 | GSE272396 | 0.006415 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, LPS&IFNg Stimulated, 6Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347315 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537705 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: Vehicle,time: 6Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399949 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537704,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347316 | GSM8399949 | GSE272396 | 0.040895 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, Vehicle, 6Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347316 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537704 |
|
1 | cell line: THP-1,genotype: WT,treatment: Vehicle,time: 12Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399951 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537702,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347318 | GSM8399951 | GSE272396 | 0.042831 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, Vehicle, 12Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347318 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537702 |
|
1 | cell line: THP-1,genotype: WT,treatment: LPS + IFNg,time: 12Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399952 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537701,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347319 | GSM8399952 | GSE272396 | 0.008197 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, LPS&IFNg Stimulated, 12Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347319 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537701 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: Vehicle,time: 12Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399953 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537700,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347320 | GSM8399953 | GSE272396 | 0.040975 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, Vehicle, 12Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347320 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537700 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: LPS + IFNg,time: 12Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399954 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537699,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347321 | GSM8399954 | GSE272396 | 0.008107 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, LPS&IFNg Stimulated, 12Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347321 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537699 |
|
1 | cell line: THP-1,genotype: WT,treatment: Vehicle,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399955 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537698,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347322 | GSM8399955 | GSE272396 | 0.010548 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, Vehicle, 24Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347322 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537698 |
|
1 | cell line: THP-1,genotype: WT,treatment: LPS + IFNg,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399956 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537697,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347323 | GSM8399956 | GSE272396 | 0.038041 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, WT, LPS&IFNg Stimulated, 24Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347323 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537697 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: Vehicle,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399957 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537696,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347324 | GSM8399957 | GSE272396 | 0.012492 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, Vehicle, 24Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347324 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537696 |
|
1 | cell line: THP-1,genotype: IRG1 KO,treatment: LPS + IFNg,time: 24Hr | Eli Lilly and Company | Indianapolis | USA | Eli Lilly and Company | Frank,Charles,Dorsey | Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.,Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.,Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.,Assembly: GRCh37.p5,Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample | RNA extracted using Qiagen Rneasy,Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit | GSM8399958 | Illumina NovaSeq 6000 | Jul 17 2024 | cDNA | transcriptomic | RNA-Seq | total RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42537695,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25347325 | GSM8399958 | GSE272396 | 0.009876 | THP-1 | Public on Jul 17 2024 | Jul 16 2024 | 9606 | THP-1, IRG1 KO, LPS&IFNg Stimulated, 24Hr, rep3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25347325 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42537695 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409070 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654485,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392596 | GSM8409070 | GSE272681 | 0.005274 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML008, bonemarrow, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392596 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654485 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409071 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654484,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392595 | GSM8409071 | GSE272681 | 0.005289 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML008, blood, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392595 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654484 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409072 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654483,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392606 | GSM8409072 | GSE272681 | 0.002097 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML009, bonemarrow, time point 1, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392606 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654483 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409073 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654482,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392594 | GSM8409073 | GSE272681 | 0.003219 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML009, blood, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392594 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654482 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409074 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654481,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392604 | GSM8409074 | GSE272681 | 0.001938 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML010, bonemarrow, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392604 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654481 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409075 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654480,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392593 | GSM8409075 | GSE272681 | 0.201446 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML010, blood, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392593 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654480 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409076 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654479,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392592 | GSM8409076 | GSE272681 | 0.001049 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML010, blood, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392592 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654479 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409077 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654478,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392601 | GSM8409077 | GSE272681 | 0.000818 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML012, bonemarrow, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392601 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654478 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409078 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654477,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392600 | GSM8409078 | GSE272681 | 0.001736 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML012, blood, time point 1, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392600 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654477 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409079 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654476,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392599 | GSM8409079 | GSE272681 | 0.001403 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML012, blood, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392599 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654476 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409080 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654475,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392598 | GSM8409080 | GSE272681 | 0.000684 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML013, bonemarrow, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392598 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654475 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409081 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654474,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392597 | GSM8409081 | GSE272681 | 0.005274 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML013, blood, time point 1, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392597 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654474 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409082 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654473,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392602 | GSM8409082 | GSE272681 | 0.001335 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML013, blood, time point 3, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392602 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654473 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409083 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654472,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392603 | GSM8409083 | GSE272681 | 0.004755 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML014, bonemarrow, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392603 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654472 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409084 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654471,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392605 | GSM8409084 | GSE272681 | 0.002793 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML014, blood, time point 2, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392605 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654471 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409085 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654470,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392607 | GSM8409085 | GSE272681 | 0.005156 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML015, bonemarrow, time point 1, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392607 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654470 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409086 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654469,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392618 | GSM8409086 | GSE272681 | 0.003067 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML018, blood, time point 1, Batch 1 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392618 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654469 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409087 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654468,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392608 | GSM8409087 | GSE272681 | 0.003906 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML012, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392608 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654468 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409088 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654467,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392609 | GSM8409088 | GSE272681 | 0.001403 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML013, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392609 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654467 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409089 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654466,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392610 | GSM8409089 | GSE272681 | 0.001798 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML014, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392610 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654466 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409090 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654465,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392611 | GSM8409090 | GSE272681 | 0.004298 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML015, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392611 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654465 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409091 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654464,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392612 | GSM8409091 | GSE272681 | 0.000477 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML018, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392612 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654464 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409092 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654463,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392613 | GSM8409092 | GSE272681 | 0.000582 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML019, bonemarrow, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392613 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654463 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409093 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654462,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392614 | GSM8409093 | GSE272681 | 0.005141 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML019, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392614 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654462 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409094 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654461,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392615 | GSM8409094 | GSE272681 | 0.000784 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML019, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392615 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654461 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409095 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654460,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392616 | GSM8409095 | GSE272681 | 0.001248 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML020, bonemarrow, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392616 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654460 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409096 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654459,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392617 | GSM8409096 | GSE272681 | 0.001248 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML020, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392617 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654459 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409097 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654458,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392653 | GSM8409097 | GSE272681 | 0.004269 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML020, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392653 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654458 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409098 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654457,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392643 | GSM8409098 | GSE272681 | 0.002452 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML020, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392643 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654457 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409100 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654455,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392645 | GSM8409100 | GSE272681 | 0.000361 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML021, bonemarrow, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392645 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654455 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409101 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654454,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392646 | GSM8409101 | GSE272681 | 0.000545 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML021, bonemarrow, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392646 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654454 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409102 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654453,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392647 | GSM8409102 | GSE272681 | 0.012685 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML021, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392647 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654453 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409103 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654452,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392648 | GSM8409103 | GSE272681 | 0.004385 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML021, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392648 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654452 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409104 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654451,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392649 | GSM8409104 | GSE272681 | 0.004236 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML021, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392649 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654451 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409105 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654450,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392650 | GSM8409105 | GSE272681 | 0.005274 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML022, bonemarrow, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392650 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654450 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409106 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654449,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392651 | GSM8409106 | GSE272681 | 0.0009 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML022, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392651 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654449 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409107 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654448,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392652 | GSM8409107 | GSE272681 | 0.000028 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML023, bonemarrow, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392652 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654448 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409108 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654447,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392654 | GSM8409108 | GSE272681 | 0 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML023, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392654 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654447 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409109 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654446,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392655 | GSM8409109 | GSE272681 | 0.000545 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML023, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392655 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654446 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409110 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654445,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392656 | GSM8409110 | GSE272681 | 0.0009 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML023, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392656 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654445 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409111 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654444,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392657 | GSM8409111 | GSE272681 | 0.001403 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML024, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392657 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654444 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409112 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654443,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392658 | GSM8409112 | GSE272681 | 0.001435 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML024, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392658 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654443 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409113 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654442,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392659 | GSM8409113 | GSE272681 | 0.001049 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML025, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392659 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654442 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409114 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654441,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392660 | GSM8409114 | GSE272681 | 0.003897 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML025, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392660 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654441 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409115 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654440,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392661 | GSM8409115 | GSE272681 | 0.002703 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML027, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392661 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654440 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409116 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654439,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392662 | GSM8409116 | GSE272681 | 0.000028 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, bonemarrow, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392662 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654439 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409117 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654438,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392663 | GSM8409117 | GSE272681 | 0.000477 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, bonemarrow, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392663 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654438 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409118 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654437,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392664 | GSM8409118 | GSE272681 | 0.001443 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, bonemarrow, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392664 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654437 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409119 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654436,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392665 | GSM8409119 | GSE272681 | 0.000981 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392665 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654436 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409120 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654435,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392666 | GSM8409120 | GSE272681 | 0.000698 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, blood, time point 2, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392666 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654435 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409121 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654434,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392619 | GSM8409121 | GSE272681 | 0.001049 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML028, blood, time point 3, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392619 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654434 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409122 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654433,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392620 | GSM8409122 | GSE272681 | 0.004238 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML030, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392620 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654433 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409123 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654432,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392621 | GSM8409123 | GSE272681 | 0.001335 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML032, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392621 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654432 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409124 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654431,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392622 | GSM8409124 | GSE272681 | 0.002405 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML033, bonemarrow, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392622 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654431 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409125 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654430,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392623 | GSM8409125 | GSE272681 | 0.00202 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML033, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392623 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654430 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409126 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654429,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392624 | GSM8409126 | GSE272681 | 0 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML034, blood, time point 1, Batch 2 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392624 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654429 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409127 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654428,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392625 | GSM8409127 | GSE272681 | 0.005274 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML022, bonemarrow, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392625 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654428 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409128 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654427,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392626 | GSM8409128 | GSE272681 | 0.001403 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML024, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392626 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654427 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409129 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654426,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392627 | GSM8409129 | GSE272681 | 0.000886 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML030, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392627 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654426 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409130 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654425,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392628 | GSM8409130 | GSE272681 | 0.001901 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML030, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392628 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654425 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409131 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654424,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392639 | GSM8409131 | GSE272681 | 0 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML032, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392639 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654424 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409132 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654423,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392640 | GSM8409132 | GSE272681 | 0.00033 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML032, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392640 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654423 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409133 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654422,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392629 | GSM8409133 | GSE272681 | 0.001335 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML033, bonemarrow, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392629 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654422 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409134 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654421,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392630 | GSM8409134 | GSE272681 | 0.002405 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML033, blood, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392630 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654421 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409135 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654420,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392631 | GSM8409135 | GSE272681 | 0.000698 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML033, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392631 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654420 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409136 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654419,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392632 | GSM8409136 | GSE272681 | 0 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML034, bonemarrow, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392632 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654419 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409137 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654418,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392633 | GSM8409137 | GSE272681 | 0 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML034, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392633 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654418 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409138 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654417,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392634 | GSM8409138 | GSE272681 | 0.003894 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML034, blood, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392634 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654417 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409139 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654416,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392635 | GSM8409139 | GSE272681 | 0.005725 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML034, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392635 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654416 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409140 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654415,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392636 | GSM8409140 | GSE272681 | 0.00187 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML035, bonemarrow, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392636 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654415 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409141 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654414,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392637 | GSM8409141 | GSE272681 | 0.001201 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML035, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392637 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654414 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409142 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654413,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392638 | GSM8409142 | GSE272681 | 0.002585 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML036, bonemarrow, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392638 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654413 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409143 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654412,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392641 | GSM8409143 | GSE272681 | 0.000847 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML036, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392641 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654412 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409144 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654411,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392642 | GSM8409144 | GSE272681 | 0.004447 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML036, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392642 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654411 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409145 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654410,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392667 | GSM8409145 | GSE272681 | 0.00205 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML036, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392667 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654410 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409146 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654409,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392668 | GSM8409146 | GSE272681 | 0.001201 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML037, bonemarrow, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392668 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654409 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409147 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654408,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392669 | GSM8409147 | GSE272681 | 0.0009 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML037, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392669 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654408 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409148 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654407,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392670 | GSM8409148 | GSE272681 | 0.002358 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML037, blood, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392670 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654407 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409149 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654406,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392671 | GSM8409149 | GSE272681 | 0.006197 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML037, blood, time point 3, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392671 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654406 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409150 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654405,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392672 | GSM8409150 | GSE272681 | 0.005274 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML038, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392672 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654405 |
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1 | tissue: bonemarrow | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409151 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654404,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392673 | GSM8409151 | GSE272681 | 0 | bonemarrow | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML039, bonemarrow, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392673 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654404 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409152 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654403,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392674 | GSM8409152 | GSE272681 | 0.002554 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML039, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392674 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654403 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409153 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654402,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392675 | GSM8409153 | GSE272681 | 0.000698 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML040, blood, time point 1, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392675 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654402 |
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1 | tissue: blood | Otto-Stern-Weg 3 | Zuerich | Switzerland | ETH Zurich | Yannik,,Severin | Illumina adapters, sequences of poor quality as well as polyA and polyT sequences were removed from the raw reads using TrimGalore v.0.6.0 with cutadapt v.2.0 prior to alignment. Reads were then aligned to the human reference genome GRCh38, v93 (Ensembl) using STAR v. 2.5.3a. Read per genes were counted with featureCounts v1.5.0. Gene counts below a threshold of 20 raw counts were filtered and raw counts were normalized (DESeq2).,Assembly: GRCh38, v.93,Supplementary files format and content: AML_Severin_count_matrix_aggregated.csv | Cell pellets were lysed in TriZol and RNA was extracted Quick-RNA MiniPrep Kit by Zymo according to the manufacturers instructions.,CDNA libraries were obtained according to Picelli, S. et al. Genome Res. 24, 2033â2040 (2014). Illumina library was obtained via tagmentation using Illumina Nextera Kit. All samples were sequenced in a single run on a NovaSeq6000 (single read, 100bp, depth 20 Mio reads per sample) | GSM8409154 | Illumina NovaSeq 6000 | Jul 20 2024 | cDNA | transcriptomic | RNA-Seq | polyA RNA | Homo sapiens | GPL24676 | BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN42654401,SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX25392676 | GSM8409154 | GSE272681 | 0 | blood | Public on Jul 20 2024 | Jul 19 2024 | 9606 | Patient AML040, blood, time point 2, Batch 3 | SRA | https://www.ncbi.nlm.nih.gov/sra?term=SRX25392676 | https://www.ncbi.nlm.nih.gov/biosample/SAMN42654401 |