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Sample GSM8020012 Query DataSets for GSM8020012
Status Public on Mar 20, 2024
Title dbsc, input, rep2
Sample type SRA
 
Source name muscle
Organism Bos taurus
Characteristics tissue: muscle
cell type: satellite cells
treatment: differentiation medium
Treatment protocol Bovine satelltie cells cultured in growth medium were induced to differentiate into myofibers by replacing the growth medium with differentiation medium containing 2% horse serum.
Growth protocol Bovine satellite cells were cultured in growth medium containing 10% fetal bovine serum for up to 10 days.
Extracted molecule genomic DNA
Extraction protocol Cells were lysed to release nuclei; nuclei were sonicated; and histone-DNA complexes were immunoprecipitated with specific antibodies.
ChIP-seq libraries were prepared using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs), according to the supplier’s instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
 
Data processing Adapters were trimmed using Trimmomatic
Trimmed sequencs were aligned to the bovine genome assembly using Hisat2
The aligned reads were sorted and merged using SAMtools
Peak calling of the aligned reads was made using MACS3
Assembly: BosTau 9
Supplementary files format and content: peak files in BigWig, no peak files for Input samples
 
Submission date Jan 16, 2024
Last update date Mar 20, 2024
Contact name Honglin Jiang
E-mail(s) hojiang@vt.edu
Phone 540-231-1859
Organization name Virginia Tech
Department School of Animal Sciences
Street address Litton Reaves Hall
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
 
Platform ID GPL26012
Series (1)
GSE253395 Chromatin profiling reveals many transcriptional regulators of proliferation and differentiation of bovine satellite cells
Relations
BioSample SAMN39464040
SRA SRX23254905

Supplementary file Size Download File type/resource
GSM8020012_dbsc2_input.bw 252.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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