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Sample GSM4367470 Query DataSets for GSM4367470
Status Public on Jun 24, 2020
Title H3K27me3_Ctl
Sample type SRA
 
Source name C2C12 myoblasts
Organism Mus musculus
Characteristics strain: C3H
chip antibody: H3K27me3 (Abcam_ab6002 )
cell line: C2C12
agent: none
Treatment protocol For treatment conditions, 50 nM of bexarotene was added at the induction of differentiation.
Growth protocol Cells of the murine myoblasts cell line C2C12 (ATCC) were maintained in growth medium (GM), Dulbecco’s Modified Eagle Medium (D-MEM) supplemented with 10% Fetal Bovine Serum, at 37ºC with 5% CO2. To induce differentiation, the medium of 80% confluent cell cultures was changed to differentiation medium (DM), D-MEM supplemented with 2% horse serum, and 50 nM of bexarotene was added for treatment conditions.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked in formaldehyde and sonicated with a Bioruptor (Diagenode). DNA was precipitated with the appropriate antibody and sent for sequencing to the McGill University Genome Quebec Innovation Centre.
Genomic DNA libraries were prepared for sequencing by McGill University Genome Quebec Innovation Centre using standard Illumina protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing For H3K27me3, sequencing reads were mapped to the mouse genome build mm9 using Bowtie, allowing for 3 mismatches and reporting the single best alignment per 50bp read. Picard was used to filter out replicated reads and BAM files were converted into BED files after which aligned reads were extended by 125 bp at their 3’ end, and converted to bedgraph format using the bedtools2 package. The bedgraphtobigwig package was used for visualization of experiment results.
Genome_build: mm9
Supplementary_files_format_and_content: BAM files were converted into bedgraph format via extension of reads by 125 bp at their 3’ end using the bedtools2 package.
 
Submission date Mar 02, 2020
Last update date Jun 24, 2020
Contact name Qiao Li
E-mail(s) Qiao.Li@uottawa.ca
Organization name University of Ottawa
Department Cellular and Molecular Medicine
Street address 451 smyth road
City Ottawa
State/province Ontario
ZIP/Postal code K1H 8M5
Country Canada
 
Platform ID GPL13112
Series (1)
GSE139942 ChIP-seq profiling of myogenin and p300 occupancy in the context of rexinoid signaling during early myogenic differentiation
Relations
BioSample SAMN14257093
SRA SRX7826419

Supplementary file Size Download File type/resource
GSM4367470_H3K27me3_Ctl.bedgraph.gz 258.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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