|
| Status |
Public on Feb 03, 2017 |
| Title |
HSB_2_0nM_DMSO_GSK2879552_48h_2 |
| Sample type |
SRA |
| |
|
| Source name |
HSB2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
type: T-ALL
gender: male
treatment: DMSO
|
| Treatment protocol |
Cells were treated with DMSO or 100nM GSK2879552 for 48h
|
| Growth protocol |
Cells were seeded at 0.7 x 10^6 cells/ml. Cells were cultured in RPMI 1640 medium supplemented with 10% FBS, 100 U/ml penicillin, 100 µg/ml streptomycin, 100 µg/ml kanamycin sulfate and 2 mM L-glutamine at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the miRNeasy mini kit (Qiagen) with on-column DNase digestion. The RNA quality was checked by the Experion RNA StdSens analysis kit (Bio-Rad).
For each sample, 1µg of input material (measured with Ribogreen (Invitrogen)) was used. Libraries were constructed with the Truseq stranded mRNA protocol on the IP-star robot. During the library prep, mRNA was isolated via poly-A capture and cDNA was generated. Next, fragmentation, A-tailing, adaptor ligation and a PCR (13 cycli) were performed on them. The libraries were on average 300bp long. As quality control of the library, analysis on a bioanalyzer chip and a qPCR were done. Libraries were equimolary pooled and 2.4pM of this pool was loaded on the Nextseq500, SR75.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-sequencing of HSB2 cells treated with DMSO for 48h
|
| Data processing |
basecalling with bcl2fastq
Alignment and gene quantification on Gencode_v23 were done with STAR v2.4.2a.
DESeq2 was used for differential expression analisis, using a multifactorial design
Genome_build: hg38
Supplementary_files_format_and_content: STAR raw count data, tdt
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sofie Peirs |
| E-mail(s) |
sofie.peirs@ugent.be
|
| Organization name |
Ghent University
|
| Street address |
De Pintelaan 185
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE83128 |
Oncogenic ZEB2 activation drives sensitivity towards LSD1 inhibition in T-cell acute lymphoblastic leukemia |
| GSE90657 |
Effect of 48h treatment with 100nM GSK2879552 on T-ALL cell lines HSB2 and RPMI8402 |
|
| Relations |
| BioSample |
SAMN06068017 |
| SRA |
SRX2381344 |
