|
| 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 |
| 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) |
| GSE87279 |
Conservation and innovation in the DUX4-family gene network (ChIP-seq) |
| GSE87282 |
Conservation and innovation in the DUX4-family gene network |
|
| Relations |
| BioSample |
SAMN05806621 |
| SRA |
SRX2187102 |
