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Sample GSM300317 Query DataSets for GSM300317
Status Public on Oct 09, 2008
Title Hippocampus_male_45yrs_indiv87
Sample type RNA
 
Source name brain, hippocampus, male, 45 years
Organism Homo sapiens
Characteristics individual: 87, C
brain region: hippocampus
gender: male
age (yrs): 45
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

Data table header descriptions
ID_REF
VALUE GC-RMA normalized expression values
PLIER PLIER normalized expression values

Data table
ID_REF VALUE PLIER
1007_s_at 1.2834961 1.2578268
1053_at 0.9557085 1.173058
117_at 1.291247 0.8308416
121_at 0.96417767 0.92639756
1255_g_at 5.647092 2.780077
1294_at 1.132518 1.0526319
1316_at 0.59020233 0.78159755
1320_at 1.9868009 1.1656497
1405_i_at 0.9219776 0.9008826
1431_at 0.9903219 0.9450633
1438_at 1.7216308 1.239138
1487_at 0.9261823 0.95583695
1494_f_at 0.5932352 0.8384376
1552256_a_at 1.2895058 1.2394129
1552257_a_at 1.1055847 0.95928204
1552258_at 0.66109866 0.7511624
1552261_at 0.80571735 0.7119509
1552263_at 1.5564277 1.6020277
1552264_a_at 2.9532757 2.4869657
1552266_at 0.9937875 0.90248287

Total number of rows: 54675

Table truncated, full table size 1662 Kbytes.




Supplementary file Size Download File type/resource
GSM300317.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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