|
| Status |
Public on Jul 20, 2012 |
| Title |
IMR90-PLKO-4 |
| Sample type |
RNA |
| |
|
| Source name |
IMR-90 cells expressing empty PLKO vector
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR-90
batch: Batch 9
|
| Growth protocol |
IMR-90 cells were cultured in DMEM (Cellgro) supplemented with 15% FBS (Omega Scientific), 1% Pen Strep (GIBCO), 1% Glutamax (GIBCO) and 1% MEM NEAA (GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
viORF-expressing IMR-90 cell lines at passage 9 were seeded into five replicates at a density of 1 x 10^6 cells per 10-cm plates and harvested after 48 hr in RNAlater (Ambion). After isolation of total RNA (RNeasy, Qiagen) RNA integrity was determined using a Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
RNA was converted into cDNA, then amplified and labeled with biotinylated nucleotides by in vitro transcription to produce biotinylated cRNA, according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Samples were hybridized to Human Gene 1.0 ST arrays according to the manufacturer's instructions.
|
| Scan protocol |
Scanning of microarrays was performed by following Affymetrix protocols at the Dana-Farber Cancer Institute microarray core facility.
|
| Data processing |
The data in Batches 1-8 were normalized by RMA with a custom CDF from the Michigan Microarray group (Version 13), using the R/Bioconductor package affy. ComBat was applied to this dataset with the batch variable as annotated above. Batch 9 was normalized separately by RMA with the custom CDF from the Michigan Microarray group (Version 13), using the R/Bioconductor package affy.
|
| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
Jul 20, 2012 |
| Contact name |
Megha Padi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Arizona
|
| Department |
Molecular and Cellular Biology
|
| Street address |
1071 East Lowell St.
|
| City |
Tucson |
| State/province |
AZ |
| ZIP/Postal code |
85701 |
| Country |
USA |
| |
|
| Platform ID |
GPL15648 |
| Series (1) |
| GSE38467 |
Transcriptional perturbations caused by tumor virus proteins |
|
