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