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Sample GSM1954031 Query DataSets for GSM1954031
Status Public on Mar 01, 2016
Title MyoD_ChIP_Rep1_Rep2
Sample type SRA
Source name ChIP-Seq with MyoD antibody 6975 in mouse M&M MEF cells transduced with MyoD
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
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
BioSample SAMN04293438
SRA SRX1451507

Supplementary file Size Download File type/resource
GSM1954031_MyoD_ChIP_peaks.csv.gz 1.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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