|
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 |
|
Relations |
BioSample |
SAMN03468417 |
SRA |
SRX984580 |