|
| Status |
Public on Nov 30, 2011 |
| Title |
NIH-3T3 empty (replicate 3) |
| Sample type |
RNA |
| |
|
| Source name |
NIH-3T3 cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH-3T3
transfection: empty vector
|
| Treatment protocol |
cells were stably transfected with either TMPRSS2/ERG, FUS/ERG or EWS/ERG fusion cDNA and kept under selection for resistance to G418
|
| Growth protocol |
cells were maitained in DMEM supplemented with 10% FBS, in a humidified chamber with 5% CO2 supply
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol Reagent (Invitrogen) according to manufacturer's instuctions
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix procedures.
|
| |
|
| Hybridization protocol |
Standard Affymetrix procedures.
|
| Scan protocol |
Standard Affymetrix procedures using Gene ChIP Scanner 3000
|
| Description |
R540_Empty_P3
|
| Data processing |
RMA Background adjustment, normalization and summarization of the raw data (.CEL files) were analyzed using the R package 'aroma.affymetrix' (H. Bengtsson; K. Simpson; J. Bullard; K. Hansen, aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory, Tech Report #745, Department of Statistics, University of California, Berkeley, February 2008). The CDF annotation file used was a binary-converted version of the 'unsupported' CDF that is provided by Affymetrix (http://www.aroma-project.org/node/32).
|
| |
|
| Submission date |
Sep 29, 2011 |
| Last update date |
Nov 30, 2011 |
| Contact name |
Vera Magistroni |
| E-mail(s) |
vera.magistroni@unimib.it
|
| Phone |
+39-0264488362
|
| Fax |
+39-0264488363
|
| Organization name |
University of Milano-Bicocca
|
| Department |
Clinical Medicine and Prevention
|
| Street address |
via Cadore 48
|
| City |
Monza |
| ZIP/Postal code |
20900 |
| Country |
Italy |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE32481 |
ERG deregulation induces PIM-1 over-expression and aneuploidy in prostate epitheilial cells |
|
