Strain:F344 Gender:Male Age: 4-6 Months old tissue: brain-hippocampus
Treatment protocol
Young and aged rats were separated into home cage (Non-Trained, NT) and behaviorally-characterized groups. Aged animals in the behaviorally-characterized groups were separated into two categories, aged cognitively impaired (AI) and aged cognitively unimpaired (AU) based on their relative performance in the Morris Water Maze task as previously described (Tombaugh et al., 2005)
Growth protocol
The animals were left undisturbed for a minimum of 1 month in our facility until the beginning of behavioral testing. Rats were housed in pairs in polycarbonate cages (45 x 30 x 18 cm) with corncob bedding and maintained on a 12 h light/dark schedule (lights off at 7:00 P.M.). Food (LabDiet 5001 rodent diet; LabDiet, Brentwood, MO) and water were available ad libitum. Animal health was monitored by a veterinarian; animals showing overt signs of morbidity were removed from the study.
Extracted molecule
total RNA
Extraction protocol
Immediately after euthanasia, the dorsal half of the left hippocampus was dissected free and frozen. Subsequently, mRNA was extracted, generating ~11micrograms total RNA per hippocampal sample, labeled and hybridized to RAE-230A (Affymetrix) GeneChips according to standard protocols
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (GCOS manual, 2005, Affymetrix).
Hybridization protocol
Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Rattus Norvegus. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol
GeneChips were scanned using the Affymetrix GCS 3000 7G scan.
Description
Gene expression data from Young and Aged behaviorally characterized F344 rats
Data processing
Microarray Data Filtering: Procedures employed were similar to those used previously (Blalock et al., 2003; Blalock et al., 2004). Briefly, the Microarray Analysis Suite 5 (MAS5) algorithm was applied using Affymetrix’ Gene Chip Operating System software (GCOS v1.1). All-probe-set scaling normalization (target intensity 500) was applied, and presence-call and signal intensity values were copied to Excel for further analysis. Annotations were downloaded from the Affymetrix website (July, 2005; augmented by a rat genome database search). For gene symbols represented by > 1 probe set (repeats), the probe set with the smallest test statistic was used. Within group outliers (> 2 SD from the group mean) (Blalock et al., 2004) were treated as missing values.
