gender: male phenotype: high body weight genetic background: mixed line: DAHi tissue: tail age: 44-45 d weight: 77-42g
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted from tails using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label
biotin
Label protocol
standard protocol as per 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
CEL files were processed by the Affymetrix Power Tools (apt-probeset-genotype) using the BRLMM-P model, using manufacturer's default recommended parameters except for forcing all genders to female, due to complications for SNPs on the X chromosome. Genomic DNA SNP comparison between artificially selected high lines (BEH, DAHi, DUH, MUH, EDH, RAHi, Du6/G154 and Du6i/G80) and unselected control lines.
