7 protocols
AccessionNameType
P-GSE42987-1
bioassay_data_transformation
ID_REF = VALUE = normalized log2 signal
P-GSE42987-6
image_aquisition
The stained arrays were scanned on the Affymetrix GeneChip® Scanner 3000.
P-GSE42987-7
feature_extraction
The images were analyzed and quality control metrics recorded using Affymetrix Expression Console software version 3.0.
P-GSE42987-5
hybridization
An 80 uL hybridization cocktail containing Affymetrix spike-in controls and the fragmented, labeled cDNA was loaded onto the GeneChip® Mouse Gene 1.0 ST array. The arrays were hybridized for 17 hours at 45°C, with rotation at 60 rpm on the GeneChip® Hybridization Oven 640. The arrays were then washed and stained with a Streptavidin, R-phycoerythrin conjugate stain on the GeneChip® Fluidics Station 450. Signal amplification was assessed using biotinylated antistreptavidin.
P-GSE42987-4
labeling
The Baylor College of Medicine Genomic and RNA Profiling Core Facility used the Ambion WT Expression Kit protocol and reagents to convert total RNA into sense-strand cDNA. The cDNA is then fragmented and labeled using the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671)
P-GSE42987-3
nucleic_acid_extraction
tissue was idssected over ice and snap frozen in liquid nitrogen. Tissue was homogenized in PureZOL and RNA was purified using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad).
P-GSE42987-2
grow
mouse hippocampus dissected at either 4 weeks of age or 9 weeks of age