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Sample GSM4134962 Query DataSets for GSM4134962
Status Public on Jun 19, 2020
Title ARID1A_ChIPSeq
Sample type SRA
 
Source name hESCs H9 cells
Organism Homo sapiens
Characteristics cell type: hESCs H9 cells
antibody: 04-080 Sigma-Aldrich, Anti-BAF250a/ARID1a Antibody, clone PSG3
Treatment protocol Briefly, hESCs were fixed with methanol-free formaldehyde provided by truChIP™ Chromatin Shearing Kit (Covaris, PN 520154). Chromatin of cell lysis was sheared using truChIP™ Chromatin Shearing Kit according its manual by ME220 Focused-ultrasonicator (Covaris). The sheared chromatin was then incubated with anti-ARID1A antibody and purified by using EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, 17-10086). Chromatin DNAs quality was assessed by 2100 Bioanalyzer (Agilent Technologies)
Growth protocol H9 hESCs were routinely cultured in mTesR medium (typically 1× 106 - 1×107 cells in a matrigel-coated P10 plate).
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Base calling and quality scoring were performed in Illumina NextSeq
The reads were mapped to the human genome (UCSC hg38) using Bowtie2 (v2.3.2), PICARD (v2.10.7) function MarkDuplicates was used to identify duplicate reads
MACS2 (v 2.1.2) were used to call peaks using Input as control at FDR cut off of less than 1e-2
The signal at each base was normalized by per 10 million reads
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig file showing the normalized read signal, narrowpeak file showing the peaks
 
Submission date Oct 22, 2019
Last update date Jun 20, 2020
Contact name Lei Yang
E-mail(s) lyang7@iu.edu
Phone (317) 278-5233
Organization name Indiana University School of Medicine
Department Department of Pediatrics
Street address 1044 W. Walnut St.
City Indianapolis
State/province Indiana
ZIP/Postal code 46202
Country USA
 
Platform ID GPL18573
Series (2)
GSE139260 Genome-wide maps of ARID1A binding genes in H9 human embryonic stem cells.
GSE139343 Essential and Opposite Roles of ARID1A in Coordinating Human Cardiogenesis and Neurogenesis from Pluripotent Stem Cells
Relations
BioSample SAMN13087429
SRA SRX7036324

Supplementary file Size Download File type/resource
GSM4134962_ChIPseq_3-ARID1A-mm_S3_sorted.1.55.bw 84.8 Mb (ftp)(http) BW
GSM4134962_ChIPseq_3-ARID1A-mm_S3_vs7Input_MACS2_q1e_2.narrowPeak.gz 469.9 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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