Strain: Sprague-Dawley; Gender: Male; Age: 60 days; Tissue: cortex of rat brain
Biomaterial provider
Charles River
Treatment protocol
Non-irradiated group of animals (controls).
Growth protocol
This animal was housed in the animal care facilities of Cleveland Clinic and was exposed to 12 hour light/dark cycles with free access to food and water.
Extracted molecule
total RNA
Extraction protocol
This animal was sacrificed and the brain was quickly isolated into RNAlater (Ambion, Austin, TX) and stored in -80C until extraction. Frozen brain slices stored in RNAlater were thawed on ice, and cortex and hippocampal regions were separated. Only cortex was used, this tissue was homogenized using TRIzol reagent (Invitrogen, Carlsbad, CA). RNA extraction was then performed using a commercially available kit followed by a DNAse digestion step (Qiagen RNEasy Mini Kit, and Qiagen RNAse Free DNAse set, respectively, Valencia, CA).
Label
biotin
Label protocol
250 ng of RNA was reverse transcribed into cRNA and biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX).
Hybridization protocol
cRNA was quantified using a nanodrop spectrophotometer and the cRNA quality (size distribution) was further analyzed on a 1% agarose gel. cRNA was hybridized to the Illumina RatRef-12 v1 Expression BeadChip using standard protocols (provided by Illumina, San Diego, CA). Individual hybridizations were performed on each sample, and no pooling of samples took place.
Scan protocol
Scan and Imaging procedures adhered strictly to standard protocols provided by Illumina, San Diego, CA.
Description
none
Data processing
The summarized data from the raw microarray data were log2 transformed and processed with background correction, quantile normalization and variance stabilization (Bolstad et al, 2003). Quality control analyses were applied to detect the outlier samples.
