Limitations and possibilities of low cell number ChIP-seq

Gilfillan, Gregor D; Hughes, Timothy; Sheng, Ying; Hjorthaug, Hanne S; Straub, Tobias; Gervin, Kristina; Harris, Jennifer R; Undlien, Dag E; Lyle, Robert

doi:10.1186/1471-2164-13-645

BMC Genomics

Table 2 Genome-wide pairwise correlation coefficients of replicate ChIP experiments

From: Limitations and possibilities of low cell number ChIP-seq

	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).

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ISSN: 1471-2164

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