|
| Status |
Public on Jan 11, 2010 |
| Title |
bone marrow-hypoxia-2hours-rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow-hypoxia-2hours
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow
treatment: reduced oxygen
time: 2 hours
strain: B6C3F1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from bone marrow was isolated using Paxgene Bone Marrow as described by the manufacturere (Qiagen). RNA from the liver and spleen was isolated using Qiagen mini columns as recomemended by the manufacturer.
|
| Label |
biotin
|
| Label protocol |
The Affymetrix GeneChip One-Cycle labeling kit was used for labeling according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the standard Affymetrix protocol.
|
| Scan protocol |
The microarrays were scanned on a GeneChip Scanner 3000 according to standard procedures.
|
| Description |
B6C3F1 Mouse
|
| Data processing |
RNA expression data were analyzed using the “affy” and “limma” packages of the Bioconductor suite of microarray analysis tools available for the R statistical environment (Gentleman, 2005; Gentleman et al., 2004; Irizarry et al., 2003; R Development Core Team, 2007). Robust Microarray Analysis (RMA) background correction and quantile normalization were used to generate microarray expression values. An overall linear model was fit to the data for all sample groups and specific contrasts of interest were evaluated to generate raw p-values for each probe set on the expression array (Smyth, 2004). The Benjamini-Hochberg False Discovery Rate (FDR) method was then used to correct for multiple testing effects. Probe sets were considered to have changed qualitatively in a specific comparison if an adjusted p-value of 0.05 was obtained, their average expression intensity was above 150 in either treatment group, and they had an absolute fold change greater than 1.3.
|
| |
|
| Submission date |
Aug 25, 2009 |
| Last update date |
Jan 11, 2010 |
| Contact name |
Petra Koza-Taylor |
| E-mail(s) |
petra.h.koza-taylor@pfizer.com
|
| Organization name |
Pfizer
|
| Street address |
Eastern Point Road
|
| City |
groton |
| State/province |
CT |
| ZIP/Postal code |
06340 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE17796 |
Expression data from B6C3F1 mice treated with reduced oxygen |
| GSE17880 |
Expression data from B6C3F1 mice treated with 2-butoxyethanol and reduced oxygen |
|
