Table 2

Genome-wide pairwise correlation coefficients of replicate ChIP experiments
GM GM GM GM H3 H3 H3 H3 H3 H3 H3 H3 H3 H3 H3 H3
H3 H3 H3 H3 K27 K27 K27 K27 K27 K27 K4 K4 K4 K4 K4 K4
K27 K27 K4 K4 me3 me3 me3 me3 me3 me3 me3 me3 me3 me3 me3 me3
me3 me3 me3 me3 100k 100k 100k 20k 20k 20k 100k 100k 100k 20k 20k 20k
R1 R2 R1 R2 R1 R2 R3 R1 R2 R3 R1 R2 R3 R1 R2 R3
GM H3K27 me3 R1 1.00 0.86 0.07 −0.02 0.70 0.70 0.70 0.70 0.69 0.69 −0.05 −0.05 −0.05 0.01 0.02 0.06
GM H3K27 me3 R2 0.86 1.00 0.17 0.16 0.74 0.70 0.72 0.72 0.73 0.70 0.04 0.05 0.05 0.09 0.10 0.12
GM H3K4 me3 R1 0.07 0.17 1.00 0.95 0.01 0.02 0.01 0.02 0.02 0.03 0.68 0.67 0.69 0.57 0.63 0.51
GM H3K4 me3 R2 −0.02 0.16 0.95 1.00 0.00 −0.01 −0.01 0.00 0.01 0.00 0.72 0.71 0.74 0.59 0.64 0.49
H3K27me3 100k R1 0.70 0.74 0.01 0.00 1.00 0.95 0.97 0.96 0.96 0.94 −0.09 −0.09 −0.09 −0.06 −0.06 −0.03
H3K27me3 100k R2 0.70 0.70 0.02 −0.01 0.95 1.00 0.94 0.94 0.93 0.92 −0.09 −0.09 −0.09 −0.05 −0.05 −0.01
H3K27me3 100k R3 0.70 0.72 0.01 −0.01 0.97 0.94 1.00 0.95 0.95 0.93 −0.09 −0.09 −0.09 −0.05 −0.05 −0.02
H3K27me3 20k R1 0.70 0.72 0.02 0.00 0.96 0.94 0.95 1.00 0.95 0.93 −0.09 −0.09 −0.09 −0.05 −0.05 −0.02
H3K27me3 20k R2 0.69 0.73 0.02 0.01 0.96 0.93 0.95 0.95 1.00 0.93 −0.08 −0.08 −0.08 −0.04 −0.04 −0.01
H3K27me3 20k R3 0.69 0.70 0.03 0.00 0.94 0.92 0.93 0.93 0.93 1.00 −0.08 −0.09 −0.09 −0.04 −0.04 0.00
H3K4me3 100k R1 −0.05 0.04 0.68 0.72 −0.09 −0.09 −0.09 −0.09 −0.08 −0.08 1.00 0.86 0.88 0.70 0.76 0.59
H3K4me3 100k R2 −0.05 0.05 0.67 0.71 −0.09 −0.09 −0.09 −0.09 −0.08 −0.09 0.86 1.00 0.87 0.69 0.76 0.59
H3K4me3 100k R3 −0.05 0.05 0.69 0.74 −0.09 −0.09 −0.09 −0.09 −0.08 −0.09 0.88 0.87 1.00 0.70 0.77 0.58
H3K4me3 20k R1 0.01 0.09 0.57 0.59 −0.06 −0.05 −0.05 −0.05 −0.04 −0.04 0.70 0.69 0.70 1.00 0.66 0.56
H3K4me3 20k R2 0.02 0.10 0.63 0.64 −0.06 −0.05 −0.05 −0.05 −0.04 −0.04 0.76 0.76 0.77 0.66 1.00 0.60
H3K4me3 20k R3 0.06 0.12 0.51 0.49 −0.03 −0.01 −0.02 −0.02 −0.01 0.00 0.59 0.59 0.58 0.56 0.60 1.00

Pearson′s correlation coefficients for all pairwise sample comparisons were calculated for read depth across the genome divided into 50 kb (H3K27me3) or 10 kb (H3K4me3) non-overlapping bins. Replicate datasets derived from 100,000 cells / IP (100k) and those from 20,000 cells / IP (20k) are denoted by suffixes R1- R3. For comparison, four ENCODE datasets (two replicates each of H3K27me3 and H3K4me3) from the cell line GM12878, a lymphoblastoid cell line, have been included (GM; replicates denoted by R1 and R2).

Gilfillan et al.

Gilfillan et al. BMC Genomics 2012 13:645   doi:10.1186/1471-2164-13-645

Open Data