Nebnext ultra 2 library kit

Dried agarose plugs of each isolate were placed in liquid Fries media [33 (link)] and cultured for approximately 48 hours. Fungal tissue was then collected, lyophilized, and homogenized using Lysing Matrix A (MP Biomedicals) by vortexing for 3 minutes on maximum speed. Genomic DNA was extracted using the Biosprint using the manufacturer’s protocol. DNA was enzymatically fragmented using dsDNA fragmentase (New England Biolabs) and whole genome sequencing libraries were prepared using the NEBNext Ultra II Library kit (New England Biolabs) according the recommended protocol. NEBNext Multiplex Oligos for Illumina were used to uniquely index libraries and were subsequently sequenced at the Beijing Genome Institute (BGI) on an Illumina HiSeq 4000. Raw sequencing reads of each isolate were uploaded to the NCBI short read archive under BioProject PRJNA398070.

Patient‐derived cells were cross‐linked with 1% methanol‐free formaldehyde for 10 min. After quenching with glycine, cells were washed three times with PBS and the cell pellet was frozen in liquid nitrogen. For analysis, the cell pellet was thawed and treated with four units MNase per 1 × 10⁶ cells for 15 min. MNase was stopped with 10× covaris buffer, and the chromatin was sheared for an additional 15 min with the S2 covaris device. The soluble chromatin was then recovered and subjected to a background‐minimizing pre‐clearing step with an unspecific IgG antibody. For each ChIP assay, an equivalent of 3 × 10⁶ cells was used. After the IP, chromatin was digested with RNaseA and proteinase K. From the purified DNA sequencing, libraries were generated with the NEBNext Ultra library preparation kit (NEB). ChIP‐seq of both CTCF and EBF1 was done with the SimpleChIP‐seq kit from Cell Signaling Technology according to the manufacturer's instructions. After purification of the DNA, libraries were cloned with the NEBNext Ultra II library kit (NEB). The antibodies used for ChIP‐seq were H3K4me1 (Abcam ab8895), H3K4me3 (Abcam ab8580), H3K9ac (Active Motif 39137), H3K9me3 (Abcam ab8898), H3K27ac (Abcam ab4729), H3K27me3 (Abcam ab6002), H3K36me3 (Abcam ab9050), H3 (Abcam ab1791), CTCF (Active Motif 61311), and EBF1 (Sigma SAB2501166) and are listed in Appendix Table S4.