|
| Status |
Public on Apr 02, 2012 |
| Title |
Runx-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
myoblasts transduced with lentivirus carrying Runx3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RD cells
|
| Treatment protocol |
RD cells were infected with titer-matched amounts of either RUNX1-, ZNF238-, miR-206- or GFP-expressing lentiviruses, allowed to recover in growth media for 24 hours, and then shifted to differentiation media for 72 hours. Each condition was performed with 3 independent biological replicates.
|
| Growth protocol |
RD cells were obtained from ATCC (American Type Culture Collection) in approximately 1990, and all analyses have been performed on cells that originated from low passage number frozen aliquots. 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 |
Feb 01, 2012 |
| Last update date |
May 17, 2012 |
| Contact name |
Janet M. Young |
| E-mail(s) |
jayoung@fhcrc.org
|
| Phone |
206 667 1471
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Division of Human Biology
|
| Lab |
Tapscott
|
| Street address |
1100 Fairview Avenue N., C3-168, P.O. Box 19024
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE35491 |
miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells (Illumina) |
| GSE35921 |
miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells |
|
