Fig. 1: ENCODE assays by year. | Nature

Fig. 1: ENCODE assays by year.

From: Perspectives on ENCODE

Fig. 1

Accumulations of assays over the three phases of ENCODE. 3D chromatin structure includes ChIA-PET (62 experiments), Hi-C (31), and chromatin conformation capture carbon copy (5C, 13). Chromatin accessibility includes DNAase-seq (524), assay for transposase-accessible chromatin using sequencing (ATAC-seq, 129), transcription activator-like effector nuclease (TALEN)-modified DNAase-seq (40), formaldehyde-assisted isolation of regulator elements with sequencing (FAIRE-seq, 37) and micrococcal nuclease digestion with deep sequencing (MNase-seq, 2). DNA methylation includes DNAme arrays (259), WGBS (124), reduced-representation bisulfite sequencing (RRBS, 103), methylation-sensitive restriction enzyme sequencing (MRE-seq, 24) and methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq, 4). Histone modification includes ChIP–seq (1,605) on histone and modified histone targets. Knockdown transcription includes RNA-seq preceded by small interfering RNA (siRNA, 54), short hairpin RNA (shRNA, 531), clustered regularly interspaced short palindromic repeats (CRISPR, 50) or CRISPR interference (CRISPRi, 77). RNA binding includes enhanced cross-linking immunoprecipitation (eCLIP, 349), RNA bind-n-seq (158), RNA immunoprecipitation sequencing (RIP-seq, 158), RNA-binding protein immunoprecipitation-microarray profiling (RIP-chip, 32), individual nucleotide-resolution CLIP (iCLIP, 6) and Switchgear (2). Transcription includes RNA annotation and mapping of promoters for the analysis of gene expression (RAMPAGE, 155), cap analysis gene expression (CAGE, 78), RNA paired-end tag (RNA-PET, 31), microRNA-seq (114), microRNA counts (114), more classical RNA-seq (900) and RNA-microarray (170), including 112 experiments at single-cell resolution. Transcription factor (TF) binding is ChIP–seq on non-histone targets (2,443). Other assays include genotyping array (123), nascent DNA replication strand sequencing (Repli-seq, 104), replication strand arrays (Repli-chip, 63), tandem mass spectrometry (MS/MS, 14), genotyping by high-throughput sequencing (genotyping HTS, 12) and DNA-PET (6) can be looked at in detail at

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