title: GSM8504127: 22Rv1_EM-seq; Homo sapiens; OTHER
library_construction_protocol: Cells were harvested, crosslinked, and lysed to isolate intact nuclei. Methyl-Micro-C library: Nuclei were treated with MNase and proximity ligation was performed with a biotinylated bridge. Ligated DNA products underwent end preparation (NEB, E7546S) and methylated adapters (NEB, E7165AAVIAL) are added. After enriching ligated products, oxidation of methylated and hydroxy-methylated cytosines and deamination of unprotected unmethylated cytosines were performed using EM-seq conversion module (NEB, E7125S). Methyl-Micro-C library was generated by performing indexing PCR and sequenced using Illumina NovaSeq sequencing systems, following the guidelines of the manufacturer. EM-seq library: EM-seq library was generated as previously reported (PMID: 34140313), and the library was sequenced with Illumina NovaSeq sequencing platforms. NOMe-seq library: NOMe-seq library was generated using M.CviPI methyltransferase (NEB, M0227B) to methylate GpCs as previously described [PMID: 29605855]. Bisulfite treatment was used to methylate CpGs, and the library was generated using IDT xGen Methyl-seq kit (IDT, 10009824) and sequenced with Illumina NovaSeq sequencing platforms.