|
Status |
Public on Aug 31, 2018 |
Title |
JQ1_50_rep1 |
Sample type |
SRA |
|
|
Source name |
Triple-negative breast cancer (TNBC) cell line, JQ1 50 nM for 18 hrs
|
Organism |
Homo sapiens |
Characteristics |
cell line: MDA-MB-231 agent: JQ1 dose: 50 nM time: 18 hrs platform: Epigenomics Core of Weill Cornell
|
Treatment protocol |
MDA-MB-231 cells were treated with DMSO or compounds (final DMSO concentration 1‰) for 18 hours.
|
Growth protocol |
MDA-MB-231 cells were grown in DMEM with 10% FBS at 37°C in the incubator containing 5% CO2.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using NucleoSpin® RNA (Macherey-Nagel). RNA libraries were prepared for sequencing using standard Illumina protocols by sequencing cores.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequencing short reads were mapped to the reference genome assembly (Hg19) using TopHat (version 2.0.8) HT-seq was used to find read counts across genes. Differentially expressed genes were identified using DESeq2 Tdf files were generated using IGVTools. Genome_build: Hg19 Supplementary_files_format_and_content: tab-delimited text file containing raw counts and tdf files for each sample
|
|
|
Submission date |
Jun 10, 2018 |
Last update date |
Aug 31, 2018 |
Contact name |
MING-MING ZHOU |
E-mail(s) |
ming-ming.zhou@mssm.edu
|
Phone |
212-659-8652
|
Organization name |
Icahn School of Medicine at Mount Sinai
|
Street address |
1425 madison ave
|
City |
new york |
State/province |
NY |
ZIP/Postal code |
10029 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE115550 |
Spatially Constrained Tandem Bromodomain Inhibition Bolsters Sustained Repression of BRD4 Transcriptional Activity for TNBC Cell Growth |
|
Relations |
BioSample |
SAMN09389057 |
SRA |
SRX4190671 |