|
| Status |
Public on Jun 20, 2012 |
| Title |
Embryo Irx3-/-;Irx5+/- rep 04 |
| Sample type |
RNA |
| |
|
| Source name |
mouse embryo of Irx3-/-;Irx5+/- genotype
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Irx3-/-;Irx5+/-
tissue: heart
developmental stage: embryo
age: E12.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using PicoPure RNA Isolation Kit (Arcturus Bioscience) and quality was assessed with Agilent RNA 6000 Pico Chips on a Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
Biotynilated cDNA were prepared using NuGEN WT-Ovation FFPE System V2 and NuGEN Encore Biotin Module (NuGene) protocols, from 1ng total RNA
|
| |
|
| Hybridization protocol |
2.5ug of fragmented cDNA were hybridized to Affymetrix GeneChip mouse gene 1.0 ST.
|
| Scan protocol |
the arrays were scanned using the scan protocol GCS3000
|
| Description |
Gene expression data from Irx5-/- embryos
Irx3-/-;Irx5+/-_04.CEL
|
| Data processing |
Arrays were normalized together for array-specific effects using Affymetrix “Robust Multi-Array” (RMA) normalization, as implemented in the R affy package. For statistical analyses, all probe sets where none of the groups had an average log2 intensity greater than 3.0 were removed. Linear models were fitted for each gene using the limma package in R/Bioconductor, which was also used to calculate moderated t-statistics and the associated P-values. The FDR-adjusted P-values were adjusted for multiple testing by controlling for false-discovery rate using the Benjamini-Hochberg method.
The array values are given as log2(normalized array intensity), where average probeset expression level is typically between 7 and 8 (and where 8.0 = 2x the expression level of 7.0). Differential expression p-values and fdr-adjusted p-values are calculated as described above.
|
| |
|
| Submission date |
Jun 20, 2012 |
| Last update date |
Jun 20, 2012 |
| Contact name |
Nathalie Gaborit |
| E-mail(s) |
[email protected]
|
| Organization name |
the J. David Gladstone Institute
|
| Street address |
1650 Owens Street
|
| City |
San Francisco |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE38826 |
Cooperative and antagonistic roles for Irx3 and Irx5 in cardiac morphogenesis and postnatal physiology |
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