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Sample GSM1654609 Query DataSets for GSM1654609
Status Public on Apr 10, 2015
Title Myoblast-GATA4-ChIP
Sample type SRA
Source name Skeletal muscle myoblast
Organism Mus musculus
Characteristics strain: STOCK Myf5tm1Pas/J
culture: Growth medium
chip antibody: Anti-GATA4 (Santa Cruz, C-20; Santa Cruz, H-112; eBioscience, eBioevan)
Growth protocol Satellite cell-derived myoblasts were cultured in growth medium (Ham’s/F10, 20% FBS, 20 ng/ml bFGF) on collagen-coated plate.
Extracted molecule genomic DNA
Extraction protocol Myoblasts were fixed with 1% formaldehyde. Extracted protein-DNA complex was fragmented to 200-500 bp then immunoprecipitated with cocktail of anti-GATA4 antibody or control IgG using Protein G Sepharose 4 Fast Flow.
Two-barcoded TruSeq ChIP DNA libraries were prepared as Illumina recommended.
250-300 bp products were subjected to HiSeq 2500 Sequencing System to generate paired-end 150 bp sequence reads.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
Data processing Basecalls performed using CASAVA version 1.8.
Following procedures were performed using Galaxy platform.
Identical reads in each data were counted as one read to eliminate PCR duplicates.
Reads were mapped to mouse GRCm38/mm10 genome by bowtie with allowing up to four mismatches.
Peaks were called using MACS in comparison of GATA4- with IgG-ChIP-seq data
Genome_build: mm10
Supplementary_files_format_and_content: BED files were generated using Galaxy.
Submission date Apr 09, 2015
Last update date May 15, 2019
Contact name Genomics Center
Organization name University of Minnesota
Lab 1-202 Nils Hasselmo Hall
Street address 312 Church Street SE
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
Platform ID GPL17021
Series (1)
GSE67703 ChIP-seq of GATA4 in mouse skeletal muscle myoblasts
BioSample SAMN03468417
SRA SRX984580

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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