|
| Status |
Public on Jan 03, 2012 |
| Title |
untransduced |
| Sample type |
SRA |
| |
|
| Source name |
untransduced
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: Combined anti-DUX4 C-terminus rabbit polyclonal antibodies MO488 and MO490
cell type: human myoblasts
|
| Growth protocol |
Primary myoblasts grown in F-10 nutrient media, 20% FBS, 1% Pen/Strep, 10 ng/ml bFGF and 1 µM Dexamethasone.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Illumina ChIP-seq sample prep kit protocol with two modifications: (1) DNA fragments ranging from 150 to 300 bp were selected at the gel-selection step; (2) 21 cycles of PCR were performed at the PCR amplification step instead of 18.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequence reads were obtained using the Illumina Genome Analyzer IIx. Reads were aligned to human genome (hg18) using BWA. Peaks are called using in-house developed R package peakSig.
|
| |
|
| Submission date |
Nov 21, 2011 |
| 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 |
GPL10999 |
| Series (1) |
| GSE33838 |
DUX4 activates germline genes, retroelements and immune-mediators: Implications for facioscapulohumeral dystrophy |
|
| Relations |
| SRA |
SRX107285 |
| BioSample |
SAMN00760376 |
