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Sample GSM1348541 Query DataSets for GSM1348541
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
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
BioSample SAMN02689292
SRA SRX490452

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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