|
| Status |
Public on Jan 16, 2009 |
| Title |
U2OS_control_shRNA_pLenti_2_2007 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS control shRNA_pLenti_2007
|
| Organism |
Homo sapiens |
| Characteristics |
Cells: U2OS, Treatment: infected with control shRNA_pLenti, blasticidin selection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from U2OS control shRNA cells using TRIzol reagent (Invitrogen) and purified further using the RNeasy MinElute Cleanup kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Illumina TotalPrep RNA amplification kit (Ambion) per manufacturer's instructions
|
| |
|
| Hybridization protocol |
standard as recommended by the Illumina user manual
|
| Scan protocol |
standard as recommended by Illumina
|
| Description |
Total RNA was isolated from U2OS control shRNA transductants using TRIzol (Invitrogen) and DNase treated with the TURBO DNA-free kit (Ambion). RNA samples were further purified using the RNeasy MinElute Cleanup kit (Qiagen). Integrity of the RNA was evaluated using the Agilent 2100 BioAnalyzer. 500 ng of RNA was used to perform in vitro transcription in the presence of biotin UTP with the Illumina TotalPrep RNA amplification kit (Ambion). The amplified, labeled RNA (1.5 _g) was then hybridized in triplicate to an Illumina Whole-Genome Sentrix Human-6 v2 Expression BeadChip, and detected according to the Illumina user manual.
|
| Data processing |
The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized.
|
| |
|
| Submission date |
Dec 04, 2008 |
| Last update date |
Jan 15, 2009 |
| Contact name |
Richard C Scarpulla |
| Organization name |
Northwestern Medical School
|
| Department |
CMB
|
| Street address |
303 East Chicago Ave.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL6102 |
| Series (1) |
| GSE14428 |
Physiological defects associated with short hairpin RNA-mediated silencing of PGC-1-related coactivator (PRC) |
|
