|
| Status |
Public on Mar 01, 2016 |
| Title |
Mock_MyoD_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with GFP
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblasts
genotype/variation: MyoD-/-; Myf5-/-
|
| Treatment protocol |
M&M MEF cells were infected in DMEM + 10% FBS media containing polybrene at a final concentration of 8 µg /ml. After 12 hours, media was replaced with fresh DMEM +10% FBS, and after 24 hours (from infection) the cells were transitioned to Differentiation media (DMEM containing insulin and transferin). Cells were harvested after 20 hours in Differentiation media. Negative controls for MyoD and Myf5 ChIPs were cells infected with lenti-GFP.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed in 1% formaldehyde for 11 minutes, quenched with glycine, lysed, and then sonicated to generate final DNA fragments of ~150–600 bp.
The soluble chromatin was diluted 1:10 and pre-cleared with a 1:1 Protein A:G slurry for 2 hours at 4oC. Chromatin was mixed with antibody overnight at 4oC, then Protein A:G beads for 2 hours. Beads were washed and de-crosslinked overnight for ~16 hours in 1%SDS, 0.1M NaHCO3 and 70 ug Proteinase K.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to human genome hg19 using BWA (0.7.5)
Peaks were called using in-house peak calling algorithm
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq peaks in csv format
|
| |
|
| Submission date |
Nov 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Tapscott |
| E-mail(s) |
stapscot@fredhutch.org
|
| Organization name |
Fred Hutch Cancer Research Center
|
| Department |
Human Biology
|
| Lab |
Tapscott
|
| Street address |
1100 Fairview N. Ave
|
| City |
Seattle |
| State/province |
WASHINGTON |
| ZIP/Postal code |
98103 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE75370 |
Distinct activities of Myf5 and MyoD indicate sequential roles in skeletal muscle lineage specification and differentiation (ChIP-Seq) |
| GSE75632 |
Distinct activities of Myf5 and MyoD indicate sequential roles in skeletal muscle lineage specification and differentiation |
|
| Relations |
| BioSample |
SAMN04293443 |
| SRA |
SRX1451512 |
