|
| Status |
Public on Aug 31, 2018 |
| Title |
MS645_500_rep0 |
| Sample type |
SRA |
| |
|
| Source name |
Triple-negative breast cancer (TNBC) cell line, MS645 500 nM for 18 hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
agent: MS645
dose: 500 nM
time: 18 hrs
platform: Mount Sinai sequencing core
|
| 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 |
SAMN09389059 |
| SRA |
SRX4190669 |
