The rats were sacrificed at postnatal day 14 (P14) via rapid decapitation followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The RNA was divided into two aliquots earmarked for transcriptional profiling using different microarray platforms. The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.
Label
biotin
Label protocol
One aliquot from each sample was transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures.
Hybridization protocol
One aliquot from each sample was transcriptionally profiled using Affymetrix Rat Expression Set 230 (RAE230A) microarray according to standard manufacturer’s procedures.
Scan protocol
not provided
Description
Failed Quality Control
Data processing
For our current analyses, the ReadAffy() function (from R package affy version 1.54.0; Gautier et al. 2004, Bioinformatics. 20: 307–315) was used to read the data from the hippocampal Affymetrix .CEL files into R studio (version 3.4.0). An expression set was generated using the Robust Multi-Array Average method (RMA: Irizarry et al. 2003, Biostatistics. 4: 249–264). Using a custom .cdf (Dai et al. 2005, Nucleic Acids Res. 33: e175) we summarized the probe signals into probesets for the RAE230A chip (“rae230arnentrezgcdf_19.0.0”) which mapped the probe sequences to Entrez Gene IDs (downloaded from http://nmg-r.bioinformatics.nl/NuGO_R.html on Jan 2017, release date Nov 2015). We re-annotated the data according to Official Gene Symbol using the function org.Rn.egSYMBOL() from the R package org.Rn.eg.db (version 3.4.1; Carlson 2017, http://bioconductor.org/packages/org.Rn.eg.db/), and then removed rows lacking annotation. During quality control, we found consistent irregularity associated with one subject (bLR subject X6_RN230_HC_P14_F15_L03.CEL) and it was removed prior to further analyses. The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.
Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats
Data table header descriptions
ID_REF
VALUE
Expression set: Background corrected, log(2) transformed, quantile normalized hybridization signal for each sample for each set of probes representing a particular gene (Annotation: Entrez ID + _at)
