|
| Status |
Public on Sep 24, 2020 |
| Title |
PEER DAC Rep3 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
T-ALL cell line PEER
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PEER
treatment: Decitabine
tissue: T-ALL cell line
|
| Treatment protocol |
Cell lines were treated with 1μM Decitabine or DMSO control for 48h
|
| Growth protocol |
Cell lines were cultured in RPMI-1640 medium supplemented with 10 or 20% fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using the miRNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA sequencing reads were aligned to GRCh38 using STAR (version 2.4.2a)42 and quantified on Gencode v24.
Normalization of counts was done using DESeq2.
Genome_build: hg38
|
| |
|
| Submission date |
Jul 29, 2020 |
| Last update date |
Sep 24, 2020 |
| Contact name |
Juliette Roels |
| E-mail(s) |
roels.juliette@gene.com
|
| Phone |
6505807476
|
| Organization name |
Genentech
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE155337 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [RNAseq_DAC_celllines] |
| GSE155339 |
Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN15666615 |
| SRA |
SRX8843182 |
