|
| Status |
Public on Jul 10, 2014 |
| Title |
Control siRNA Veh rep1 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human breast adenocarcinoma
cell line: MCF7
passages: 20-30
|
| Treatment protocol |
After 2 days of hormone deprivation, MCF7 cells were treated with 10 nmol/L 17-β-estradiol (Sigma-Aldrich) for 2 hours. The cells were harvested for RNA upon Vehicle (Veh) or estrogen (E2) treatment and negative control siRNA (siCont), BRD4 siRNA (siBRD4) or JQ1 treatment. 150 nM JQ1 was pretreated to the cells 30 mins before estrogen treatment. JQ1 treated cells were also transfected with negative control siRNA.
|
| Growth protocol |
MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) with 10% bovine growth serum (Thermo Scientific). For estrogen induction experiments, after one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Sigma).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol mediated RNA isolation method was used for harvesting RNA.
500 ng RNA was used for library preparation and libraries were made using the kit TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS–122–2002)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The reads were mapped to the human reference transcriptome (UCSC HG19) using Bowtie2 2.1.0 (Langmead and Salzberg, 2012).
Read counts for each sample and each gene were aggregated using a custom Ruby script.
DESeq (version 1.14.0) was used for the measuring differential expression (Anders and Huber, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited text file with normalized read counts.
|
| |
|
| Submission date |
Mar 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven A Johnsen |
| E-mail(s) |
sjohnsen@alumni.mayo.edu
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Department of General, Visceral and Pediatric Surgery
|
| Street address |
Robert-Koch-Straße 40
|
| City |
Göttingen |
| State/province |
Niedersachsen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE55922 |
Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation [RNA-Seq] |
| GSE55923 |
Bromodomain protein BRD4 is required for estrogen receptor-dependent transcription and enhancer activation |
|
| Relations |
| BioSample |
SAMN02689292 |
| SRA |
SRX490452 |
