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Sample GSM3032377 Query DataSets for GSM3032377
Status Public on Mar 07, 2018
Title CTRL_NO_FP_rep3
Sample type SRA
 
Source name RNAPII was profiled in RMG-1 clone in ARID1A-WT condition
Organism Homo sapiens
Characteristics cell line: RMG-1
chip antibody: Custom, rabbit polyclonal, raised against N terminus of RNAPII
Treatment protocol Doxycicline (2ug/ml, 72 hours) was used to induced the knock-down of ARID1A with a TET-inducible shRNA.
Growth protocol RMG-1 cells were maintained in DMEM/F12 50/50 medium (Corning) supplemented with 10% (v/v) of TET-free fetal bovine serum (Clontech) or super calf serum (GEMcell) and 2 mM of L-glutamine (Corning).
Extracted molecule genomic DNA
Extraction protocol NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (ChIPseq, ATAC-seq): BWA
alignment (RNAseq): STAR
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)
 
Submission date Mar 06, 2018
Last update date Mar 07, 2018
Contact name Marco Trizzino
E-mail(s) marco.trizzino83@gmail.com
Phone 4845983902
Organization name The Wistar Institute
Department Gene expression and regulation
Street address 3601 Spruce street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL18573
Series (1)
GSE104545 The ARID1A tumor suppressor controls global transcription via pausing of RNA Polymerase II
Relations
BioSample SAMN08640854
SRA SRX3769516

Supplementary file Size Download File type/resource
GSM3032377_CTRL_NO_FP_rep3.bw 83.5 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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