|
Status |
Public on Feb 01, 2017 |
Title |
C2C12_MMH6_488_489 |
Sample type |
SRA |
|
|
Source name |
cultured mouse myoblasts (C2C12)
|
Organism |
Mus musculus |
Characteristics |
genotype/variarion: MMH_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.
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|
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
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|
|
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 |
SAMN06205238 |
SRA |
SRX2464262 |