Matrix – ENCODE

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Assay

Biosample

	TF ChIP-seq	Histone ChIP-seq	Control ChIP-seq	DNase-seq	total RNA-seq	Mint-ChIP-seq	polyA plus RNA-seq	shRNA RNA-seq	ATAC-seq	CRISPR RNA-seq	microRNA-seq	snRNA-seq	snATAC-seq	Control eCLIP	DNAme array	eCLIP	small RNA-seq	RNA Bind-n-Seq	WGBS	ChIA-PET	long read RNA-seq	Control Mint-ChIP-seq	RAMPAGE	RNA microarray	intact Hi-C	genotyping array	CAGE	microRNA counts	siRNA RNA-seq	Repli-seq	RRBS	in situ Hi-C	CRISPRi RNA-seq	long read scRNA-seq	Repli-chip	PAS-seq	Bru-seq	GM DNase-seq	RIP-seq	FAIRE-seq	BruChase-seq	RIP-chip	polyA minus RNA-seq	RNA-PET	WGS	scRNA-seq	PRO-cap	PRO-seq	BruUV-seq	MS-MS	5C	dilution Hi-C	DNA-PET	icSHAPE	seqFISH	GRO-cap	MRE-seq	MeDIP-seq	SPRITE	iCLIP	5' RLM RACE	MNase-seq	Switchgear	icLASER	Circulome-seq
cell line	3122	867	918	231	213	146	198	522	205	461	39	2	38	259	91	250	111		18	137	56	25	30	73	30	75	53	8	113	92	57	61	77	2	21	10	45	46	45	26	28	32	20	26	15	4	24	22	14	13	13	4	6	6		4	4	4		3		2	2	2
K562	771	19	279	7	61		19	263	64	250	2		3	150	3	145	7		1	9	4		1	10	1	2	9	1	50	6	1	1	77				2	46	8	3	2	10	3	6	4		6		1	6	2		3	2		2	1	1		3		1		2
HepG2	825	15	93	2	6		11	259	2	211	2		3	109	3	105	3		2	4	3			6	1	2	6	1		6	2	1					2			1	2	4	3	2	3				1		1			2
A549	254	86	88	14	11		27		6				2		2		9		1	2				2		2	3			2	1	6								1			1	3	1			3
HCT116	43	17	23	16	17	92	1		17		2		7		2					33	1	16		1	17			1			1	8					18				2						14	16	1
GM12878	189	15	32	1	5		13		2		2		3		3		6		1	6	4		1	7	1	2	6	1		6	2	5				1	2		7	1	2	11	3	2		2			1	5	2	2	3	2		2	1	1				1

tissue	439	2175	665	945	447		399		225		305	390	292	2	121	2	67		162	1	112		104	2	82	7	17	101			17	8		61	1	14				7					12	15									5
dorsolateral prefrontal cortex	59	188	61	56	120						43										9				1																														5
adrenal gland	8	39	13	33	26		11		8		23	59	15	2	5	2	2		5		19		4		2			2			1			28
heart	6	81	17	39	21		16		7		25	49	17				1		10		6		2					8
heart left ventricle	16	84	17	10	9		2		15		5	54	65		3				4		4		2		10			2			1
liver	42	91	29	24	3		20		8		7	8	8		1		1		9				2					7			1

primary cell	76	525	140	565	243	715	151		83		52	1	29		38		24		7	60	6	129	28	58	19	37	30	1		12	27	19			7	13	4			4	4		11	4		8	1		2			3
naive thymus-derived CD4-positive, alpha-beta T cell		16	3	16	5	74	8		2		2		2							2		13			2
T-cell		11	3	63	7	18	1		6										1	4		3													1
naive thymus-derived CD8-positive, alpha-beta T cell				13	2	66	6		3		1		1							1		12
CD14-positive monocyte	2	21	4	8		41	8						2				1		1			8			2		1																1
macrophage		4	2		78		14

whole organisms	1292		1285		272		80	105																			19									16									3																2				1
whole organism	1292		1285		268		72	105																			15									15									3																2				1
carcass					4		8																				4									1

in vitro differentiated cells	58	265	61	45	55	78	23		41		17	2	11		6		12		24	2	17	13	6	6		4	1	5			2	9		1	34	1							1			3				1									3
dendritic cell		11			25				30																																					3													3
motor neuron		18	6		9				10										10													9
endodermal cell	1	8	3	2	3	12	2				2		1						2		8	2													2	1
neuronal stem cell		27	5	1			2										1		2																1
neural progenitor cell	4	12	2	1	1	6					1				1		1			1		1	1					1							3

cell-free sample																		213
cell-free sample																		213

organoid	7		7	2		48																8
brain	4		4	2		30																5
nephron	3		3			18																3

technical sample					1																7
technical sample					1																7

Experiment Matrix

Showing 23534 results