Mouse MHC-adapted Cryptococcus neoformans H99W
For genomic DNA libraries, the standard CTAB protocol for DNA isolation was followed,. Next, the DNA was sheared using an M220 Covaris sonicator with microTUBE AFA (SKU: 520045) and the following parameters: duty factor: 20%, peak/displayed power 50 W, cycles/burst: 200, duration: 65 sec, and temperature: 20 C. The NEBNext Ultra II DNA Library Prep with Sample Purification Beads kit (cat. no. E7103S) was used to generate Illumina libraries, using the maximum recommended input (1 g) to minimize PCR cycles. Libraries were sequenced on an Illumina HiSeq 4000 with paired-end reads of 100 bp for each strain, including the parent H99W strain. Each library consisted of roughly 1013 million sequences, with output files in fastq format.