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Sample GSM2326756 Query DataSets for GSM2326756
Status Public on Feb 01, 2017
Title Sample_2-hDUX4-WITHdoxy-MO
Sample type SRA
Source name cultured mouse myoblasts (C2C12)
Organism Mus musculus
Characteristics genotype/variarion: HDUX4 codon-altered
treatment: DOXYCYCLINE
antibody: MO488, MO489 (anti-hDUX4)
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 Sample_2-hDUX4-WITHdoxy-MO:Sample_1-hDUX4-WITHdoxy-HA_peaks.xls
Data processing Filtered out reads containing at least 'N' in sequence and trimed the as soon as 2 of 5 nucleotides has quality encoding less than “4” (phred score 20). Dropped reads that are less than 36nt.
Aligned reads using Subread 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
Submission date Sep 22, 2016
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)
GSE87279 Conservation and innovation in the DUX4-family gene network (ChIP-seq)
GSE87282 Conservation and innovation in the DUX4-family gene network
BioSample SAMN05806621
SRA SRX2187102

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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