|
| Status |
Public on Jun 12, 2008 |
| Title |
Uninduced RUNX1-ER, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
NIH3T3 retrovirally transduced with inducible Human RUNX1 construct in pBabe-puro
|
| Organism |
Mus musculus |
| Characteristics |
NIH3T3 (p16/p19arf null) confluent cell cultures, harvested after 24hrs treatment
|
| Treatment protocol |
All samples were treated with ethanol alone (0.2%) or 4-OHT tamoxifen (0.1mM) in ethanol for 24 hours prior to RNA extraction.
|
| Growth protocol |
All cultures were grown to confluence (7 days) in DMEM under standard conditions. The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Rneasy Mini kit (Qiagen) according to the manufacturers' protocol
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array in the GeneChip Hybridization Oven 640. Arrays were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Comparative study of gene targets regulated by overexpression of the different Runx family members
|
| Data processing |
The raw data were generated with GeneChip Operating Software (GCOS). Data was normalised with Robust Multichip Average (RMA) method using Bioconductor module Affy implemented into the automated FunAlyse pipeline in the Sir Henry Wellcome Functional Genomics Facility. Differential expression was calculated using RankProducts method.
|
| |
|
| Submission date |
Jun 10, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Pawel Herzyk |
| E-mail(s) |
pawel.herzyk@glasgow.ac.uk
|
| Phone |
00441413303180
|
| Organization name |
University of Glasgow
|
| Department |
College of Medical, Veterinary and Life Sciences
|
| Lab |
Glasgow Polyomics
|
| Street address |
Wolfson Wohl Cancer Research Centre, Garscube Estate
|
| City |
Bearsden |
| ZIP/Postal code |
G61 1QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE11732 |
Runx transcriptional program for control of cell adhesion and survival |
|
| Relations |
| Reanalyzed by |
GSE119085 |
