|
| Status |
Public on Jul 02, 2024 |
| Title |
DND_DMSO_8H_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
DND41
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T-ALL
treatment: DMSO
time: 8Hour
|
| Treatment protocol |
DND-41 and MOLT-4 cells were treated with 100nM ACBI-1 or DMSO. At 8 hours post treatment, total RNA were harvested.
|
| Growth protocol |
DND-41 and MOLT-4 cells were cultured in RPMI-1640 medium supplemented with 10% 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-T7 |
| |
|
| 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 ACBI treated vs 2 DMSO control samples (2 ACBI treated vs 2 DMSO control with 2 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes
|
| |
|
| Submission date |
Apr 25, 2023 |
| Last update date |
Jul 02, 2024 |
| 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 |
GPL29480 |
| Series (2) |
| GSE230589 |
RNA-seq analysis after 8hr of ACBI-1 treatment on DND-41 and MOLT-4 cells. |
| GSE230594 |
Oncogenic roles of SWI/SNF chromatin remodeling factors: therapeutic targets in T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN34370381 |
| SRA |
SRX20097848 |
