PPI testing used 120dB (40ms) startle, prepulses of 75 or 80dB (20ms), 65dB background, prepulse-startle latency of 100ms, and inter-trial-time 15-30s. Scores were averaged across three sessions, PPI calculated as [(PA–PP)/(PA)] × 100, and the mean of 75dB and 80dB trials was used. 6 of 12 mice were tested per strain every other day for 5d at PND50.
Growth protocol
Six mouse strains were used: C3H/HeJ; BALB/cJ; C57BLKS/J; C57BL/6J and C57L/J (JAX, Bar Harbor, ME, USA) spanning the range of PPI.19 PND40 mice were housed 6 per cage with a 12 hr light/dark cycle (0700-1900h), at 21±1°C , 50-60% humidity, food and water ad libitum.
Extracted molecule
total RNA
Extraction protocol
Mice were sacrificed on PND60. RNA was prepared as previously described dissected and snap frozen (-80°C) whole striatum, hippocampus, and brainstem using TRIzol® reagent. RNA quality was determined using the Agilent BioAnalyzer with no RIN <7.7, prepared for hyrbidization and hybridized and scanned at The Centre for Applied Genomics (TCAG) at SickKids, Toronto, Ontario, Canada.
Label
biotin
Label protocol
as per the User Manual: GenChip 3' IVT Express kit: Enzo IVT kit as per Toronto Centre for Applied Genomics standard labeling protocol
Hybridization protocol
as per the User Manual: GenChip 3' IVT Express kit: EukGE-WS2v4 of Toronto Centre for Applied Genomics standard hybridization protocol
Scan protocol
as per the User Manual: GenChip 3' IVT Express kit: using Affymetrix Genechip Scanner 3000 as per standard protocol used by Toronto Centre for Applied Genomics
Description
pooled tissue from 3 mice
Data processing
The raw array data was investigated for distributional and spatial homogeneity. No artifacts or outliers were detected. The data were loaded into R (v2.6.1) using the affy package (v1.16.0) of the BioConductor open-source project, and pre-processed using the GCRMA variant of the RMA algorithm implemented in the gcrma package (v2.10.0) of BioConductor. Transcriptome-wide correlation analysis between PPI and mRNA relied on Spearman’s rho and linear modelling analysis, simultaneously fitting 18 arrays per tissue to the model: y=b+(m)x(PPI), where y is GCRMA pre-processed signal intensity, b the expression level, PPI levels for a given strain, and m is the slope. Probesets were annotated using Affymetrix NetAffx (v27)21 and FDR-adjusted p-value (q-value)(Storey and Tibshirani, 2003) using the limma software package (v.2.12.0) and followed by a Bayesian moderation of standard error (Smyth, 2004); correlations and q-values were calculated and candidate genes selected on the combined q-values from the three brain regions: -log|q(Hippocampus) x q(Striatum) x q(Brainstem)|.
RNA expression across 6 strains of mice in relation to prepulse inhibition testing, as described in: Pdxdc1 (pyridoxal-dependent decarboxylase domain containing 1) modulates pre-pulse inhibition of acoustic startle in the mouse
