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Sample GSM3566508 Query DataSets for GSM3566508
Status Public on Sep 01, 2022
Title HAP1_RNA-seq_WT_shCHAF1A_Testosterone_r5
Sample type SRA
 
Source name cell line
Organism Homo sapiens
Characteristics library: RNA-seq
cell line: HAP1
replicate: 5
knockout: WT
knockdown: CHAF1A
drug_treatment: Testosterone
Growth protocol HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.
Extracted molecule polyA RNA
Extraction protocol RNA was isolated with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description RNA-seq for wild type HAP1 cell line with shRNA against CHAF1A, treated with Testosterone, replicate 5
Data processing Reads were trimmed with Trimmomatic, aligned to the GRCh37/hg19 human genome assembly using Bowtie1 and quantified transcript isoforms from Ensembl version 75 using BitSeq with default parameters. Read counts per gene are the maximum counts per isoform.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file contains read counts for each sample for each gene
 
Submission date Jan 17, 2019
Last update date Sep 01, 2022
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL20301
Series (2)
GSE125219 Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies [RNA-Seq]
GSE125221 Histone chaperone CAF-1 is a synthetic lethal vulnerability in the context of ARID1A deficiencies
Relations
BioSample SAMN10764646
SRA SRX5258215

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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