|
| Status |
Public on Feb 28, 2011 |
| Title |
MIN6 HMGN3a OE rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
MIN6 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MIN6 cells
genotype/variation: HMGN3a OE
|
| Treatment protocol |
Retroviral infection with appropriate construct in the presence of polybrene at the concentration of 5 µg/ml and subsequent selection with puromycin at the concentration of 1 µg/ml for 7 days. Cells were grown 24hr without selection prior to RNA collection.
|
| Growth protocol |
DMEM 10%FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent followed by clean up on Rneasy kit with DnaseI treatment on the columns (Qiagen).
|
| Label |
biotin
|
| Label protocol |
Hybridization of biotin-labeled cRNA fragment to Mouse Genome 430 2.0 array, washing, staining with streptavidin–phycoerythrin (Molecular Probes), and signal amplification were performed according to the manufacturer’s instructions at the Laboratory of Molecular Technology (LMT, Frederic, NCI).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human (Mouse) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affimetrix GeneChip Scanner 3000 controlled by Affymetrix Microarray AGCC 2.0.
|
| Description |
expression data from MIN6 cells
|
| Data processing |
Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor. RMA data processing includes background correction, quantile normalization, and expression summarization. Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.
|
| |
|
| Submission date |
Feb 27, 2011 |
| Last update date |
Mar 04, 2011 |
| Contact name |
Leila Taher |
| E-mail(s) |
leila.taher@uni-rostock.de
|
| Organization name |
University of Rostock
|
| Street address |
Ernst-Heydemann-Str. 8
|
| City |
Rostock |
| ZIP/Postal code |
18057 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE27546 |
Effects of HMGN variants on cellular transcription profile |
|
