|
| Status |
Public on Nov 20, 2023 |
| Title |
2h_DMSO_rep1 |
| 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_2h_DM-1
|
| 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 |
SAMN33425820 |
| SRA |
SRX19486684 |
