Whole genome sequencing of the Tallyho/Jng-MU mouse
"High quality genomic DNA was extracted from the liver of a male TH mouse from our colony using Qiagen Genomic tip 100 per G Kit, Valencia, CA. Genomic DNA 1 microg was sheared using Covaris S2 instrument, Woburn, MA to about 350 bp and used to construct a sequencing library using Illumina DNA Sample Preparation Kit, San Diego, CA according to the manufacturers recommended protocol. The library was quantified using Qubit flourimetry Life Technologies and sized on an Agilent Bioanalyzer, Santa Clara, CA. Eight pmoles of library was amplified using Illumina cBot cluster station and then sequenced on an Illumina HiSeq 1000 in the Marshall University Genomics Core Facility. Three sequencing runs, one 2x50 bp paired end and two 2x100 bp paired end, were performed in order to obtain adequate depth of coverage. Sequencing reads were aligned to the C57BL 6J B6 reference genome, GRCm38, mm10 using Bowtie v2.1.0."
alignment_software
BowTie2 2.1.0