|
| Status |
Public on Sep 15, 2015 |
| Title |
Sensitive 5.3 line Rep 2 [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Sensitive 5.3 line
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: haematopoietic progenitors
cell line: 5.3S
cultured in: 0.1% DMSO
phenotype: BET inhibitor sensitive
|
| Treatment protocol |
Cell lines were grown in 0.1% DMSO or 600nM of I-BET151
|
| Growth protocol |
Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
DMSO5-3B
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the mouse genome (Ensembl Release 75, Feb 2014) using Subread
Reads were assigned to genes using featureCounts and normalised with voom. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file of raw read counts and normalized expression values for all Samples
|
| |
|
| Submission date |
Nov 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE63681 |
Genome wide expression analysis of BET inhibitor resistance [RNA-seq] |
| GSE63683 |
iBET resistance |
|
| Relations |
| SRA |
SRX747320 |
| BioSample |
SAMN03145740 |
