. Author manuscript; available in PMC: 2024 Feb 21.

Published in final edited form as: Nat Rev Genet. 2020 Nov 26;22(4):235–250. doi: 10.1038/s41576-020-00300-0

Table 1 |.

Data types generated by selected single-omics methods

Data type	Bulk-cell methods	Single-cell methods
Gene expression	RNA-seq^41,166,167 DNA microarrays^37–39	scRNA-seq¹⁶⁸
DNA accessibility	DNase-seq⁵² ATAC-seq⁵⁴	scDNase-seq⁵⁷ scATAC-seq^55,56
Nucleosome positioning	MNase-seq⁷⁷	scMNase-seq⁷⁸
Histone modifications	ChIP–seq^88,89 ACT-seq¹⁰³ CUT&RUN¹⁶⁹ CUT&TAG¹⁰⁴ ChIL-seq¹⁰²	scChIP–seq⁹⁹ scChIC–seq¹⁰⁰ iACT-seq¹⁰³ scCUT&RUN¹⁰¹ CUT&TAG¹⁰⁴ CoBATCH¹⁰⁵ scChIL-seq¹⁰²
DNA methylation	BS-seq¹⁷⁰ RRBS¹⁷¹ MeDIP-seq¹⁷² MethylCap-seq¹⁷³	scBS-seq¹¹⁹ scRRBS¹⁷⁴
Chromatin contacts	Hi-C¹³⁶ Hi-ChIP¹⁷⁵ ChIA-PET¹⁷⁶	scHi-C^{121,125,143–146}

ACT-seq, antibody-guided chromatin tagmentation sequencing; ATAC-seq, assay for transposase-accessible chromatin sequencing; BS-seq, bisulfite sequencing; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIC–seq, chromatin immunocleavage followed by sequencing; ChIL-seq, chromatin integration labelling sequencing; ChIP–seq, chromatin immunoprecipitation followed by sequencing; CoBATCH, combinatorial barcoding and targeted chromatin release; CUT&RUN, cleavage under targets and release using nuclease; CUT&TAG, cleavage under targets and tagmentation; DNase-seq, DNase I hypersensitive site sequencing; Hi-C, high-throughput chromosome conformation capture; iACT-seq, indexed antibody-guided chromatin tagmentation sequencing; MeDIP-seq, methylated DNA immunoprecipitation sequencing; MethylCap-seq, methyl-CpG binding domain-based capture and sequencing; MNase-seq, micrococcal nuclease digestion deep sequencing; RNA-seq, RNA sequencing; RRBS, reduced representation bisulfite; sc, single-cell.