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Table 1 Different assays for functional genomics, common protocols, format of the data after processing, and application to the GRN

From: Thinking BIG rheumatology: how to make functional genomics data work for you

Assay Protocol Processed data format Direct application to GRN
Gene expression RNA-seq, microarray Table of samples (columns) by genes (rows) Output
Chromatin state ChIP-seq, ATAC-seq List of peaks Nodes
Chromatin interactions Hi-C, ChIA-PET, GAM Matrix of interactions Edges
DNA methylation BS-seq List of methylated sites Nodes
Single-cell technology scRNA-seq Table of cells (columns) by genes (rows) Discriminate different GRNs
  1. GRN gene regulatory network, RNA-seq RNA-sequencing, ChIP-seq chromatin immunoprecipitation followed by high-throughput sequencing, ATAC-seq Assay for Transposase Accessible Chromatin followed by high-throughput sequencing, Hi-C high-throughput chromosome conformation capture, ChIA-PET Chromatin Interaction Analysis by Paired-End Tag Sequencing, GAM genome architecture mapping, BS-seq bisulfite sequencing, scRNA-seq single-cell RNA-sequencing