DNA isolation from mouse ear skin sample. Digestion overnight and DNA precipitation by Isopropanol. Sample clean-up by phenol/chloroform extraction and resuspended in 1xTE buffer.
Label
biotin
Label protocol
As per the manufacturer (Affymetrix)
Hybridization protocol
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing
Two Affymetrix Mouse Diversity Genotyping Arrays were processed in the presence of 197 other arrays of the same design from two NCBI GEO datasets (GSE36409 and GSE61660). Calls were made with Affymetrix Power Tools version version 1.17.0 using the command. apt-probeset-genotype -o results_brlmm-p_all_dir_v7 -c MOUSEDIVm520650.CDF --a quant-norm.sketch=50000,pm-only,brlmm-p.CM=1.bins=100.mix=1.bic=2.HARD=3.SB=0.75.KX=0.2.KH=0.3.KXX=-0.1.KAH=-0.1.KHB=-0.1.transform=MVA.AAM=2.0.BBM=-2.0.AAV=0.06.BBV=0.06.ABV=0.06.copyqc=0.00000.wobble=0.05.CSepThr=4.CSepPen=0.1.KYAH=-0.05.KYHB=-0.05.KYAB=-0.1.AAY=9.ABY=9.5.BBY=9.copytype=-1.clustertype=2.ocean=0.00001.MS=0.1 --read-models-brlmmp Mouse.models --summaries --chrX-probes Mouse.chrXprobes --chrY-probes Mouse.chrYprobes --special-snps Mouse.specialSNPs *.CEL . The command was taken from the Affymetrix mouse vignette at http://www.affymetrix.com/estore/support/developer/powertools/changelog/VIGNETTE-Mouse-WGSA-genotyping.html.affx . Array annotation files were downloaded from the Affymetrix website (http://www.affymetrix.com/Auth/support/downloads/library_files/mouse_diversity_analysis.zip) . All SNPs were filtered by maximum p-value (0.01) and calls that were homozygous but differed between samples.
