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Sample GSM7060707 Query DataSets for GSM7060707
Status Public on Nov 20, 2023
Title 72h_DMSO_rep2
Sample type SRA
 
Source name Jurkat cells
Organism Homo sapiens
Characteristics cell line: Jurkat
cell type: T-ALL
treatment: DMSO
Treatment protocol The cells were treated with DMSO or dTAG-13 for 1h, 2h, 4h, 8h, 16h, 24h, 48h or 72h. Total RNAs were then harvested.
Growth protocol TAL1-FKBP12 Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.
Extracted molecule total RNA
Extraction protocol Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description SC3_72h_DM-2
Data processing RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 DMSO control vs 2 dTAG KD samples for each of the timepoint (2 DMSO control vs 2 dTAG KD samples with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes, featureCount read count for all samples
 
Submission date Feb 23, 2023
Last update date Nov 20, 2023
Contact name Tze King Tan
Organization name National University of Singapore
Department Cancer Science Institute
Lab Takaomi Sanda Lab
Street address 14 Medical Drive
City Singapore
ZIP/Postal code 117599
Country Singapore
 
Platform ID GPL28038
Series (2)
GSE225939 RNA-seq analysis after the treatment with DMSO or dTAG-13 in TAL1-FKBP12 Jurkat cells
GSE225941 Regulatory mechanisms and context-dependent roles of TAL1 in TALL
Relations
BioSample SAMN33425803
SRA SRX19486701

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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