Deeply Profiled Cell Lines – ENCODE

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Cell Line (batch identifier)

	PRO-cap	intact Hi-C	in situ Hi-C	GRO-cap	dilution Hi-C	Histone ChIP-seq	Mint-ChIP-seq	TF ChIP-seq	RIP-chip	RIP-seq	eCLIP	iCLIP	ATAC-seq	DNase-seq	FAIRE-seq	GM DNase-seq	MNase-seq	5C	ChIA-PET	Bru-seq	BruChase-seq	BruUV-seq	CAGE	CRISPR RNA-seq	CRISPRi RNA-seq	PAS-seq	RAMPAGE	RNA microarray	RNA-PET	long read RNA-seq	microRNA counts	microRNA-seq	polyA minus RNA-seq	polyA plus RNA-seq	shRNA RNA-seq	siRNA RNA-seq	small RNA-seq	total RNA-seq	DNAme array	MRE-seq	MeDIP-seq	RRBS	WGBS	Repli-chip	Repli-seq	DNA-PET	genotyping array	snATAC-seq	WGS	icLASER	icSHAPE	MS-MS
Caco-2	1	1				5	6	2						3				1	2	2	2	1						1		1		1						1	1			1					1	1
ENCBS095ZZD	1	1												1					2	2	2	1								1		1						1
ENCBS072CVQ	1													1						2	2	1								1		1						1										1
ENCBS257JWV							6

Calu3	1	1					6	1						1					1	2	2	1								1		1						1										1
ENCBS992CLK	1	1												1					1	2	2	1								1		1						1
ENCBS961PLX	1													1						2	2	1								1		1						1										1
ENCBS827USO							6

H9						35	18	1						8					1									1		1		1		2				1		1		1	1	1			1	1	1
ENCBS808UWK						19
ENCBS532LWE						15
ENCBS399JWQ						10								1																																	1

HepG2		1	1			15		842	2		124		2	3	1			1	5	2	2	1	6	188				7	2	3	1	2	3	11	243		3	7	3	1		2	2		6		2	3	3		1
ENCBS114ENC								42						1																									2	1		1					1
ENCBS638AAA						1		26										1										1
ENCBS621TAB											26

K562	6	1	1	2		20		821	6	26	164	7	58	10	3	46	1	2	11	2	2	1	9	237	74		1	12	6	4	1	3	3	19	258	34	8	62	3	2	1	1	1		6	3	2	3	4	1	1	6
ENCBS476EKR								126					1																																			2
ENCBS039ENC								67						1			1		2									1											1							3
ENCBS175JIH											51

WTC11							6	90					2	1					6	1						1				7		1						10
ENCBS448BXM								15
ENCBS474NOC																										1				7		1						2
ENCBS593PKA																										1				7		1						2

mammary epithelial cell		1	2		1	27		3						4					1	2	2	1	1					2		1		3	1	3			1	2	3	1	1	1	2				3
ENCBS091ENC						12		2																															1				1
ENCBS045GHW						11		2
ENCBS956YQM		1																	1	2	2	1								1		1						1