Computational protocol: Mouse genotypes drive the liver and adrenal gland clocks

Similar protocols

Protocol publication

[…] Whole exome sequencing was performed on the Illumina Hiseq2000 platform. The Burrows-Wheeler Aligner was used to align the mouse strains sequences to the NCBI reference sequence (NCBI37/mm9). The final BAM files were used as input for SOAPsnp in order to identify single nucleotide variations ( and ). In order to predict which of the variants could have the most deleterious effect on the protein activity the Grantham Matrix Score (GMS) was determined for each nonsynonymous SNV () and DAVID applied to annotate genes belonging to the radical group. Other procedures were performed in R and Bioconductor. Whole exome sequencing data is available at the European Nucleotide Archive under the Study code: PRJEB11861 (http://www.ebi.ac.uk/ena/data/view/PRJEB11861). […]

Pipeline specifications

Software tools BWA, SOAPsnp
Application WES analysis
Organisms Mus musculus
Chemicals Amino Acids, Nucleotides