Supplemental Material for Han et al., 2018

Figure S1. Identification of altered methylation in CG, CHG and CHH contexts following tissue culture
Figure S2. Identification of context specific DMRs
Figure S3. Comparisons of DNA methylation in multiple contexts for CG and CHG only DMRs
Figure S4 Methylation changes induced by tissue culture are common to many independent samples
Figure S5 Associations between DMRs and gene expression
Figure S6. Inheritance of DNA methylation changes following tissue culture
Figure S7 correspondence of DMRs among individual R1 siblings
Table S1 Sample metadata and sequencing metrics
Table S2 Total context-specific DMRs per sample
Table S3 Non-redundant list of CG and CHG DMRs categorised by direction, consistency and specificity
Table S4 Gene loci that may lose heterochromatin
File S1 Supplemental methods: Sequence capture probe maize genome conversion from AGPv2 to AGPv4