|
| Status |
Public on Apr 12, 2011 |
| Title |
4_day_old_wildtype_mouse_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: FVB
developmental stage: newborn (4-day-old)
tissue: hippocampus
genotype/variation: Prnp+/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, treated with DnaseI (Ambion) and purified with the RNeasy Mini kit (Qiagen). RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was quantified with a NanoDrop 1000 spectrophotometer (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
A 10μg-amount of each total RNA sample was labeled according to the standard one-cycle amplification and labeling protocol (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Labeled cRNA was hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays, containing 22,690 probesets corresponding to approximately 14,000 well-characterized mouse genes. Hybridized arrays were stained and washed (GeneChip Fluidics Station 450).
|
| Scan protocol |
Hybridized arrays were scanned with the GeneChip Scanner 3000 7G.
|
| Data processing |
Cell intensity values and probe detection calls were computed using the Affymetrix GeneChip Operating Software (GCOS). Further data processing was performed in the R computing environment (http://www.r-project.org/) version 2.8.0 with BioConductor packages (http://www.bioconductor.org/). Robust Multi-Array Average (RMA) normalization was applied. Data were then filtered based on Affymetrix detection call and probeset intensity, so that only probesets that had a present call and intensity value >100 in at least one of the arrays were retained. Statistical analysis was performed with limma. P-values were adjusted for multiple testing using Benjamini and Hochberg’s method to control the false discovery rate. Genes with adjusted P values below 0.05 were considered differentially expressed.
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| |
|
| Submission date |
May 06, 2010 |
| Last update date |
Apr 12, 2011 |
| Contact name |
Paola Roncaglia |
| Organization name |
SISSA/ISAS (International School for Advanced Studies)
|
| Department |
Neurobiology
|
| Street address |
via Bonomea 265
|
| City |
Trieste |
| State/province |
TS |
| ZIP/Postal code |
34136 |
| Country |
Italy |
| |
|
| Platform ID |
GPL8321 |
| Series (1) |
| GSE21718 |
Developmental influence of the cellular prion protein on the gene expression profile in mouse hippocampus |
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