|
| Status |
Public on Aug 29, 2013 |
| Title |
RDMD |
| Sample type |
SRA |
| |
|
| Source name |
Rhabdomyosarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Rhabdomyosarcoma
chip antibody: MyoD
|
| Treatment protocol |
To differentiate myoblasts, cells were allowed to achieve 90% confluency prior to a shift in culture media to Dulbecco’s modified media containing 1% horse serum with insulin (10 μg/mL) and transferrin (10 μg/mL). Differentiation media was changed every 24 h for up to 5 day.
|
| Growth protocol |
RD cells were obtained from the American Type Culture Collection (ATCC) and early passage cells were used in all experiments. RD cells were maintained in Dulbecco modified Eagle medium (DMEM) with 10% bovine calf serum and 1% penicillin-streptomycin (Gibco).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary myoblast samples were collected in growth medium at low density, and both primary myotubes and RD cells were collected after being cultured in differentiation medium (72 h for myotubes, 24 h for RD cells).
Libraries were generated from immunoprecipitated DNA as outlined in the Illumina DNA Library Construction Kit protocol except that 21 rounds of PCR were performed for amplification, and DNA fragments ranging from 200-350 bp were isolated during size selection on agarose gel.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
MyoD ChIP-Seq in Rhabdomarcoma
|
| Data processing |
Sequence reads were obtained using the GApipeline program (version 0.3.0).
Reads were aligned to human genome hg19 using BWA (0.5.9)
Peaks were called using an in-house peak calling algorithm
Genome_build: hg19
Supplementary_files_format_and_content: MyoD ChIP-Seq peaks in ENCODE broadPeak format
|
| |
|
| Submission date |
Aug 28, 2013 |
| 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 (2) |
| GSE50413 |
Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors (MyoD ChIP-Seq profiling) |
| GSE50415 |
Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors |
|
| Relations |
| BioSample |
SAMN02338762 |
| SRA |
SRX341012 |
