|
| Status |
Public on Sep 01, 2009 |
| Title |
H-ras KO 0 hrs, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Mus musculus cell lines from the appropriate ras genotype
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Fibroblasts
genotype: H-ras -/- KO
condition: after starvation
|
| Treatment protocol |
Fibroblasts of different mice wild type, H-ras, N-ras and HN-ras KOs that were serum-starved for 24 hours, and them gene expression data from wild type (WT Control) and ras KO genotypes were obtained before (0 hour) or after short term (1hour, G0/G1 transition) or mid-term (8 hour, mid-G1 progression) post-starvation incubation of the cell cultures in the presence of 20% fetal bovine serum (FBS).
|
| Growth protocol |
Pre-confluent cultures of at least two separate cell lines belonging to each of the ras-related genotype(s) under study (WT, H-ras-/- and N-ras-/- and H-ras-/-/N-ras-/-) were harvested and their RNA extracted for subsequent analysis using Affymetrix high density oligonucleotide microarrays MGU74Av2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized according to the manufacturer's protocol on Mus musculus MGU74Av2 GeneChip high-density oligonucleotide microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Fibroblasts of different mice wild type, H-ras, N-ras and HN-ras KOs that were serum-starved for 24 hours, and them gene expression data from wild type (WT Control) and ras KO genotypes were obtained before (0 hour) or after short term (1hour, G0/G1 transition) or mid-term (8 hour, mid-G1 progression) post-starvation incubation of the cell cultures in the presence of 20% fetal bovine serum (FBS).
|
| Data processing |
The data were analyzed using the RMA method for background correction, normalization and signal calculation of the complete dataset (39 microarrays). The method was use ir R with BioConductor tools.
|
| |
|
| Submission date |
Feb 13, 2009 |
| Last update date |
May 28, 2009 |
| Contact name |
Javier De Las Rivas |
| E-mail(s) |
jrivas@usal.es
|
| Phone |
34 923 294819
|
| Organization name |
Cancer Research Center (CiC-IBMCC)
|
| Department |
CSIC and University of Salamanca
|
| Lab |
Bioinformatics and Functional Genomics
|
| Street address |
Campus Miguel de Unamuno
|
| City |
Salamanca |
| ZIP/Postal code |
37001 |
| Country |
Spain |
| |
|
| Platform ID |
GPL81 |
| Series (1) |
| GSE14829 |
Serum-dependent transcriptional networks identify distinct functional roles for H-ras and N-ras |
|
