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Sample GSM2171433 Query DataSets for GSM2171433
Status Public on Oct 17, 2016
Title RNA-seq for BRD4 knockdown cells
Sample type SRA
 
Source name PEO1 ovarian cancer cells
Organism Homo sapiens
Characteristics experiment type: RNAseq
treatment: shBRD4
Treatment protocol PEO1 cells were treated with or without 200 nM JQ1 for 72 hours or PEO1 cells were infected with lentivirus encoding short hairpin RNA to the human BRD4 gene (shBRD4) or control
Growth protocol Human ovarian cancer cell line PEO1 were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin and 100 mg/ml streptomycin. Cells were passaged every 3-4 days to complete growth medium.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-seq for BRD4 knockdown cells
Data processing RNA-Seq data analysis was done with rsem(ver. 1.2.3) and hg19 genome with UCSC known gene set.
EdgeR was used for differential expression was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes
 
Submission date May 20, 2016
Last update date May 15, 2019
Contact name Priyankara J Wickramasinghe
E-mail(s) priyaw@wistar.org
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL18573
Series (1)
GSE81698 Epigenetic targeting of immunocheckpoint PD-L1 by BET bromodomain inhibition
Relations
BioSample SAMN05157064
SRA SRX1787038

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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