|
| Status |
Public on Nov 26, 2008 |
| Title |
neocortex, 5 months mouse#2 |
| Sample type |
RNA |
| |
|
| Source name |
neocortex from B6xC3 F1 hybrid mice at 5 months of age
|
| Organism |
Mus musculus |
| Characteristics |
Strain: B6xC3 F1 hybrid
Age: 5 months
Gender: male
|
| Treatment protocol |
Control Diet: Mice were fed 24 g/wk of AIN-93M diet which has a total energy content of 16740 kJ/kg.
|
| Growth protocol |
Male B6C3F1 mice were purchased from Harlan-Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidifed water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen tissue using the TRIZOL reagent (Invitrogen, San Diego, CA) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Double-stranded DNA was then synthesized from 1 ug of mRNA using the SuperScript Choice System (Invitrogen) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, LaJolla, CA), purified with phenol-chloroform-isoamyl alchohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA usind the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.
|
| 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 |
Chips used in this study were the Affymetrix MOE 430 2.0 arrays which have 45, 037 probe sets (Affymetrix, Santa Clara, CA). cRNA (10 ug) in hybridization cocktail was placed in the chip and hybridized at 45° C for 16 hours with mixing on a rotisserie at 60 rpm. Following hybridization, the hybrization solutions were removed and the gene chips were installed in a fluidics system for washing and staining.
|
| Scan protocol |
After staining, the gene chips were read at a resolution of 3 um using a Hewlett Packard GeneArray Scanner (Affymetrix). The averaged images collected from two scanned images were used for the analysis.
|
| Description |
Gene expression data from mouse neocortex
|
| Data processing |
The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize overall variability in hybridization by a global scaling method.
|
| |
|
| Submission date |
Oct 16, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Philipp Oberdoerffer |
| E-mail(s) |
philober@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Sinclair
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE13120 |
Age-related gene expression changes in mouse neocortex |
| GSE13121 |
SIRT1 redistribution on chromatin promotes genome stability but alters gene expression during aging |
|
| Relations |
| Reanalyzed by |
GSE119085 |
