|
| Status |
Public on Mar 31, 2014 |
| Title |
Expression data from E18.5 Igf1-/- (homozygous mutant) mouse lungs - Sample 3 |
| Sample type |
RNA |
| |
|
| Source name |
Lungs from embryos at embrionic (E) stage 18.5 days post coitum (E18.5)
|
| Organism |
Mus musculus |
| Characteristics |
age: E18.5
genotype: Igf1-/- (homozygous mutant)
tissue: lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by using the Trizol (Invitrogen) method following manufacturer’s instructions. Trizol-purified RNA was then treated with RNase-free DNase I (Roche) and mRNA purified with RNeasy spin columns (Qiagen). RNA quantity and quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
|
| 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, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MOE430A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned at 3-mm density with a GeneChip® Scanner 3000 7G 4C (Affymetrix).
|
| Description |
Lungs from E18.5 were isolated from both Igf1+/+ wild type and Igf1-/- null mice and pooled to obtain RNA. Heterozygous male and female with a genetic background C57BL/6J were mated to obtain embryos at embrionic (E) stage 18.5 days post coitum (E18.5).
|
| Data processing |
To normalize and calculate gene expression signals, the RMA algorithm was used. To detect the probe-sets with differential expression, the SAM algorithm was applied, and the data was normalized using the FDR value (False discovery rate or proportion of false negatives). The final list corresponds to the 640 differentially expressed genes with a FDR<0,20 (p<0,001; 640 probe sets; 566 genes).
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| |
|
| Submission date |
Jul 16, 2009 |
| Last update date |
Mar 31, 2014 |
| 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 |
GPL8321 |
| Series (1) |
| GSE17157 |
Expression data from E18.5 Igf1 -/- (homozygous mutant) and Igf1+/+ (normal wild type control) mouse lungs |
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