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Sample GSM2054578 Query DataSets for GSM2054578
Status Public on Feb 05, 2017
Title RNA-seq for DMSO-treated cells
Sample type SRA
Source name DMSO-treated cells
Organism Homo sapiens
Characteristics cell line: OVCAR3
agent: DMSO
Treatment protocol cells were incubated with 0.5 mM ethidium uridine (EU) and treated with 125 nM vehicle control for 40min
Growth protocol Ovarian cancer cell lines were cultured in RPMI1640 medium (Corning) supplemented with 10% fetal bovine serum (FBS; Sigma), 100 U/ml penicillin, 100 ug/ml streptomycin
Extracted molecule total RNA
Extraction protocol total RNA isolated using Trizol reagent
Ovation Human FFPE RNA-Seq Multiplex System 1-8 (Nugen)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description RNA-seq for DMSO-treated cells
Data processing Chip-seq files were aligned using bowtie version 0.12.9 to human genome hg19
Peak calling was done with homer (v1.0) software with options -fdr 0.01 -style histone
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 analysis
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq processed files contain Homer peak calling output; RNA-Seq expression file contains raw counts and FPKM values for all genes
Submission date Feb 04, 2016
Last update date May 15, 2019
Contact name Priyankara J Wickramasinghe
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)
GSE77568 Inhibition of BET protein BRD4 activity synergizes with cisplatin in ovarian cancer by targeting ALDH activity through an ALDH1A1 super-enhancer and the associated enhancer RNA
BioSample SAMN04455973
SRA SRX1560787

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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