|
| Status |
Public on Jun 24, 2020 |
| Title |
C2C12_Myog_Ctl |
| Sample type |
SRA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H
tissue: C2C12 myoblasts
chip antibody: Myogenin (Santa Cruz_sc-12732X)
|
| 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 4000 |
| |
|
| Data processing |
For p300, 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. For myogenin, sequence reads were aligned to the mouse mm9 reference genome build using BWA-Mem with default parameters. 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.
Peak calling was performed with Hypergeometric Optimization of Motif EnRichment (Homer) v4.10 with -style factor and FDR of 1.0 x 10-4.
Genome_build: mm9
Supplementary_files_format_and_content: Myogenin and p300 peaks were called by HOMER and represent significant enrichment of aligned reads compared to input control.
|
| |
|
| Submission date |
Nov 05, 2019 |
| 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 |
GPL21103 |
| Series (1) |
| GSE139942 |
ChIP-seq profiling of myogenin and p300 occupancy in the context of rexinoid signaling during early myogenic differentiation |
|
| Relations |
| BioSample |
SAMN13198831 |
| SRA |
SRX7101175 |
