|
| Status |
Public on Oct 09, 2008 |
| Title |
EntorhinalCortex_male_28yrs_indiv29 |
| Sample type |
RNA |
| |
|
| Source name |
brain, entorhinal cortex, male, 28 years
|
| Organism |
Homo sapiens |
| Characteristics |
individual: 29, C
brain region: entorhinal cortex
gender: male
age (yrs): 28
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 10-200 mg of frozen, unfixed tissue using Trizol reagent (Invitrogen, Carlsbad CA), and purified using quick spin columns (Qiagen, Valencia CA). RNA quality was assessed using the Agilent BioAnalyzer (Agilent Technologies, Palo Alto, CA) and UV spectrophotometer for the presence of sharp peaks and 28S/18S RNA.
|
| Label |
biotin
|
| Label protocol |
Total RNA (10 ug) from each sample was used to generate first strand cDNA using a T7-linked-(dT)24 primer, followed by in vitro transcription using the ENZO BioArray High-Yield RNA transcript labeling kit (ENZO Farmingdale, NY) to generate biotin-labeled cRNA target.
|
| |
|
| Hybridization protocol |
Using a robotics system (Biomek FX MicroArray Plex SA System; Beckman Coultier) to optimize consistency in processing and minimize handling variability, each fragmented, biotin-labeled cRNA sample (30 mg) was individually hybridized to an Affymetrix Hg-U133 plus 2.0 chip for 16 hours and rotated at 13 rpm at 50C.
|
| Scan protocol |
The chips were scanned using an Affymetrix GeneChip Scanner 3000 7G
|
| Description |
Brain from cognitively intact individual.
|
| Data processing |
GC-RMA expression values were obtained from CEL files using GeneSpring 7.3.1 software. PLIER expression values were obtained using Expression Console software using default settings. PLIER and GC-RMA data were processed using GeneSpring 7.0 software, with default normalizations (Data transformation:set values<0.01 to 0.01; per chip: normalize to 50th percentile; per gene: normalize to median).
|
| |
|
| Submission date |
Jun 25, 2008 |
| Last update date |
Jun 26, 2019 |
| Contact name |
Nicole Claudia Berchtold |
| E-mail(s) |
nberchto@uci.edu
|
| Phone |
949 824 6071
|
| Organization name |
UC Irvine
|
| Department |
Institute for Memory Impairments and Neurological Disorders
|
| Lab |
Carl W. Cotman
|
| Street address |
1226 Gillespie Neuroscience Facility
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697-4540 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE11882 |
Gene expression changes in the course of normal brain aging are sexually dimorphic |
| GSE48350 |
Alzheimer's Disease Dataset |
|
| Relations |
| Reanalyzed by |
GSE119087 |
| Reanalyzed by |
GSE133349 |
