TABLE 2.
Selected high-throughput methods for studying host-pathogen interactions
| Methoda | Purpose | Reference(s) |
|---|---|---|
| RNA-seq | Transcript analysis | 145 |
| Dual RNA-seq | Transcript analysis of both the host and the pathogen | 146, 147 |
| scRNA-seq | Transcript analysis | 136 |
| GRO-seq | Transcription | 148 |
| PRO-seq | Genome-wide map of transcriptionally engaged Pol II | 149 |
| Nascent-seq | Transcription | 150 |
| ChIA-PET | Chromatin conformation | 151 |
| Hi-C | Chromatin conformation | 152, 153 |
| 5-C-seq | Chromatin conformation | 154 |
| DNase-seq | Open chromatin | 155 |
| ATAC-seq | Open chromatin | 156 |
| ChIP-seq | Mapping DNA regulatory elements | 157 |
| BS-seq | Genome methylation | 158 |
| RRBS-seq | Genome methylation | 159 |
| ITS1-seq | Fungi detection | 160 |
| Nano LC-MS/MS | Host and fungal quantitative proteome analysis without isolation | 161 |
a
seq, sequencing; scRNA, single cell RNA; GRO, global run-on; PRO, precision nuclear run-on; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; 5-C, chromosome conformation capture carbon copy; ATAC, assay for transposase-accessible chromatin; ChIP, chromatin immunoprecipitation; BS, bisulfite; RRBS, reduced representation bisulfite sequencing; ITS1, internal transcribed spacer 1; Nano LC-MS/MS, nanoscale liquid chromatography tandem mass spectrometry.