|
| Status |
Public on Aug 29, 2013 |
| Title |
primary human muscle myotubes rep1 |
| Sample type |
RNA |
| |
|
| Source name |
primary human muscle myotubes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human muscle myotubes
|
| Growth protocol |
Cells were collected both in growth medium at a low cell density for the myoblast condition and after 72 h at complete cellular confluence in low-serum differentiation medium for the myotube condition. Cells were maintained in DMEM with 10% bovine calf serum and 1% Pen-Strep (Gibco). Low-serum differentiation media consisted of DMEM with 1% horse serum, 1% Pen-Strep and 10 ug/mL insulin and transferrin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen RNeasy kit according to manufacturer's instruction. Quality control was performed with Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
Probe intensities were corrected, normalized, and summarized by the Lumi package of Bioconductor (Du et al., 2008). Differentially expressed genes were identified by the LIMMA package of Bioconductor (Wettenhall and Smyth, 2004).
Data was vst transformed and quantile normalized using the Lumi package of Bioconductor (Du et al., 2008).
|
| |
|
| Submission date |
Aug 28, 2013 |
| Last update date |
Apr 05, 2017 |
| 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 |
GPL10558 |
| Series (2) |
| GSE50411 |
Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors (expression) |
| GSE50415 |
Comparison of Genome-Wide Binding of MyoD in Normal Human Myogenic Cells and Rhabdomyosarcomas Identifies Regional and Local Suppression of Promyogenic Transcription Factors |
|
