RAD-Seq of Sylvilagus transitionalis: enriched fecal pellet
Fecal pellet collected from winter sampling 2-5 days after snow. Extraction with either Quick-DNA Fecal/Soil Microbe Kits, QIAamp DNA Stool Mini Kit, NucleoSpin Tissue Mini kit for DNA from cells and tissue. Extract enriched with FecalSeq enrichment to remove exogenous DNA. 3RAD Library prep with 3 enxymes: XBaI, EcoRI-HF, and NheI-HF. We prepared pools of samples and size selected for 250-800 bp fragments using a Blue Pippin. Pools required 24-30 cycles to reach the molarity (10 nM) required for sequencing. We normalized and combined all 6 pools into one library that was submitted for sequencing on two lanes of an Illumina NovaSeq SP (800 million reads) with paired-end 150 bp reads and 15% PhiX spike in at the Genomic Sciences Library at North Carolina State University.