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Sample GSM2445817 Query DataSets for GSM2445817
Status Public on Feb 01, 2017
Title C2C12_MMH6_HA
Sample type SRA
 
Source name cultured mouse myoblasts (C2C12)
Organism Mus musculus
Characteristics genotype/variarion: MMH_codon-altered
treatment: DOXYCYCLINE
antibody: anti-HA
Treatment protocol induced with 2ug/ml doxycycline treatment for 18 hours or uninduced for 18 hours, as indicated
Growth protocol C2C12, mouse myoblasts (ATCC® CRL-1772™), were grown in DMEM (Gibco/Life Technologies) supplemented with 10% fetal bovine serum (Thermo Scientific) and 1% penicillin/streptomycin (Life Technologies) and 2.6ug/ml puromycin to select for cells carrying the transgene indicated.
Extracted molecule genomic DNA
Extraction protocol Briefly, ~6x10e7 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 protein A:G beads for 2 hours. Remaining chromatin was incubated with primary antibody overnight, then protein A:G beads were added for an additional 2 hours. Beads were washed and then de-crosslinked overnight.
ChIP-seq libraries were prepared from IP samples using an Ovation Ultralow Library System kit (NuGEN Technologies., San Carlos, CA, USA).
ChIP-seq libraries were pooled (12-plex) and clustered onto two flow cell lanes.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description C2C12_MM6_488_489_vs_HA_1e-2_peaks.xls
Data processing Filtered out reads containing at least 'N' in sequence.
Aligned reads using BWA on genome build mm10.
Filtered low-quality reads (mapq score < 15).
Performed peak calling using MACS2 allowing 3 mismatch with mininum FDR=0.01.
Genome_build: mm10
Supplementary_files_format_and_content: peak
 
Submission date Jan 05, 2017
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)
GSE87282 Conservation and innovation in the DUX4-family gene network
GSE93168 Conservation and innovation in the DUX4-family gene network [MMH6 ChIP-Seq]
Relations
BioSample SAMN06205237
SRA SRX2464263

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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