|
| Status |
Public on Sep 09, 2014 |
| Title |
MEF2A_ChIP-exo [mouse] |
| Sample type |
SRA |
| |
|
| Source name |
Myoblast
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: Myoblast
chip antibody: MEF2A
chip antibody vendor: Santa Cruz Biotechnology
chip antibody cat. #: sc-313X
|
| Treatment protocol |
C2C12 were induced to differentiate in differentiation medium (DM) containing DMEM/High Glucose/L-Glutamine supplemented with 2% Horse Serum (Hyclone) and 1% Penicillin/Streptomycin for 48 hr.
|
| Growth protocol |
C2C12 were grown on gelatin coated plates in Dulbecco’s Modified Eagle Medium (DMEM) with High Glucose and L-Glutamine (Hyclone) supplemented with 10% fetal bovine serum (HyClone) and 1% Penicillin/Streptomycin (Invitrogen)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and MEF2A-DNA complexes were isolated with antibody.
Libraries were prepared according to Rhee and Pugh (2011). Briefly, after ChIP, P2 adapters were ligated to DNA fragments using T4 ligase. Lambda exonuclease was added to digest unbound DNA. Samples were eluted and sequences were extended with phi29 polymerase. P2 adapters, specific to the 5' end were added. Samples were purified, run on a gel, and samples between 120-160 bp were selcted for sequencing. Libraries were sequenced on the Illumina sequencer following the manufacturer's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: ChIP-exo
Basecalls performed using CASAVA 1.7.0
ChIP-exo reads were aligned to the mm10 or rn5 genome using BWA 0.5.9
Data were filtered using the following specifications: Picard (no duplicates) and samtools q37
peaks were called using MACS 1.4.2 (--nomodel --shiftsize=20 --to-large)
Genome_build: mm10 or rn5
Supplementary_files_format_and_content: BED files were generated using MACS and contain chrom, chromstart, chromend, peak name and score (-10*log10pvalue of peak region) columns
|
| |
|
| Submission date |
Sep 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
John C McDermott |
| E-mail(s) |
jmcderm@yorku.ca
|
| Organization name |
York University
|
| Street address |
4700 Keele Street
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M3J 1P3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE61204 |
Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq] |
| GSE61207 |
Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling |
|
| Relations |
| BioSample |
SAMN03023781 |
| SRA |
SRX695942 |
