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Fig. S1 DNA methylation of a transposable element and a highly redundant gene in the DNase I-MeDIP-SEQ fraction.

Fig. S2 Control PCR for sequence enrichment of the DNase I-MeDIP-SEQ fraction.

Fig. S3 Repeat content of the DNase I-MeDIP-SEQ fraction.

Fig. S4 Enrichment of long genes in the DNase I-MeDIP-SEQ fraction.

Fig. S5 Digital northern heat map representation of genes whose introns are in the DNase I-MeDIP-SEQ fraction.

Fig. S6 General view of enriched GO molecular functions in genes whose (a) upstream or (b) downstream region or (c) body is contained in the DNase I-MeDIP-SEQ fraction.

Fig. S7 Enriched GO molecular functions in genes whose introns are contained in the DNase I-MeDIP-SEQ fraction.

Fig. S8 Enriched GO molecular functions in genes whose exons are contained in the DNase I-MeDIP-SEQ fraction.

Fig. S9 Enriched GO molecular functions in genes whose 5′ region is contained in the DNase I-MeDIP-SEQ fraction.

Fig. S10 Enriched GO molecular functions in genes whose 3′ region is contained in the DNase I-MeDIP-SEQ fraction.

Table S1 Efficiency estimation of six chromatin extraction protocols

Table S4 List of genes from the DNase I-MeDIP-SEQ fraction whose expression was studied by RT-PCR

Table S5 Criteria chosen for redundancy features of genes

nph12026-sup-0002-TableS2.txtplain text document5960KTable S2 Coordinates of MeDIP reads mapped on v2.0 P. trichocarpa genome
nph12026-sup-0003-TableS3.xlsapplication/msexcel27KTable S3 List of primers used for semi-quantitative PCR or bisulfite sequencing