Table 1.

Summary of ENCODE3 production

Assay	Description and details	No. of experiments	No. of targets	No. of biosamples
DNA binding and chromatin modification
ChIP–seq	Chromatin immunoprecipitation sequencing
	Chromatin-associated proteins	1,343	653	151
	Histone marks	1,082	13	158
Transcription
RNA-seq	RNA sequencing
	Total RNA	224	–	209
	polyA RNA	116	–	106
	microRNA	112	–	108
	small RNA	86	–	85
	Knockdown/knockout RNA sequencing
	CRISPR	50	28	2
	CRISPR interference	77	74	1
	Short hairpin RNA	523	253	2
	Small inhibitory RNA	54	35	3
scRNA-seq	Single-cell RNA sequencing	13	—	12
RAMPAGE	RNA annotation and mapping of promoters for the analysis of gene expression	155	—	154
Chromatin accessibility
DNase-seq	DNase I cleavage site sequencing	246	—	246
	DNase-seq of genetically modified cells	46	28	1
ATAC-seq	Assay for transposase accessible chromatin using sequencing	129	—	129
DNA methylation
WGBS	Whole-genome bisulfite sequencing	132	—	129
DNAme array	DNA methylation profiling by array	154	—	151
RNA binding
eCLIP	Enhanced UV crosslinking and immunoprecipitation of RNA binding proteins (RBPs) followed by sequencing to identify bound RNAs in cells	170	117	3
RNA Bind-n-seq	In vitro method for quantifying RBP–RNA interactions and identifying binding motifs	78	78	—
3D chromatin structure
ChIA-PET	Chromatin interaction analysis by paired-end tag sequencing	49	6	29
Hi-C	Genome-wide chromosome conformation capture (all-versus-all interactions)	33	—	33
Replication timing
Repli-chip	Measures DNA replication timing using microarrays	36	—	30
Repli-seq	Measures DNA replication timing using sequencing	14	—	14

Control experiments were excluded from this table but can be found in Extended Data Table 1. Counts were obtained on 1 December 2019.