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Table 3 Genome methylation tallied over 1 kb tiled genome windows, by tissue

From: Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

No. methylated 1 kb windows

By tissue

RPKM

NB

Common

Internode explant

55, 036

92, 401

52, 566 (55.4%)

Callus

51, 886

81, 444

46, 863 (54.2%)

Regen internode

42, 511

63, 722

39, 384 (58.9%)

  1. Numbers are counts of windows called methylated compared to non-immunoprecipitated control by one of two methods: RPKM at a 1% false discovery rate, or negative binomial analysis (FDR of 10%). The P. trichocarpa genome is comprised of 378,536 windows. Percentage of common windows was calculated by dividing the total number of windows called by both methods by the total of those called by either method.