Emerging single-cell technologies and multi-omics
| Single nucleus [65, 66] | Analysis of frozen/archival tissue |
| Spatial | |
| smFISH [67] | Single-molecule fluorescent in situ hybridisation |
| ISH+amplification [68] | PLISH |
| ISH+amplification+multiplexing [69–71] | MERFISH, SCRINSHOT, STARmap (3D) |
| Oligo microarray [72] | |
| LCM capture [73, 74] | Single cells on array, captured, sequenced |
| Multi-omics | |
| Surface markers | |
| Epitope capture [75, 76] | Simultaneous sequencing of mRNA and oligo-labelled antibodies; CITE-seq, REAP-seq |
| TCR antigen specificity [77] | Oligo-tagged MHC multimer libraries |
| Epigenome | |
| scRBBS [78] | Reduced-representation bisulfite sequencing |
| scWGBS [79] | Whole-genome bisulfite sequencing |
| Parallel transcriptome and methylome [80–82] | |
| CHIP-seq [83] | Chromatin immunoprecipitation sequencing |
| ATAC-seq [84] | Assay for transposase-accessible chromatin |
| Metabolome/proteome | |
| Mass spectrometer/MALDI-TOF | Matrix-assisted laser desorption/ionisation |
| Mass cytometry [85, 86] | Cytometry TOF; panel of antibody-labelled ions |
ISH: in-situ hybridisation; LCM: laser capture microscopy; TCR: T-cell receptor; TOF: time of flight; CITE-seq: cellular indexing of transcriptomes and epitopes by sequencing; REAP-seq: RNA expression and protein sequencing; MHC: major histocompatibility complex.