Table 1 Summary of single-cell technologies that have been applied to study COVID-19

From: Single-cell immunology of SARS-CoV-2 infection

Technology

Measurement

Methodology

Capacity

Pros and cons

Number of published or preprint COVID-19 articlesa

Flow cytometryb

Protein expression

Fluorophore-conjugated antibodies; cells are sorted into liquid droplets individually and flowed through a laser beam; the light emitted by each cell informs about marker expression

High throughput (millions of cells); up to ~30 markers

Pros: determination of immune cell subsets by well-defined surface markers and antibody panels; cells can be sorted for further analysis

Cons: broad emission spectra of fluorophores

47

Mass cytometry (CyTOF)

Protein expression

Antibodies conjugated to heavy-metal isotopes; cells are nebulized, and the metal-conjugated antibodies are ionized; signals are detected by a time-of-flight mass spectrometer

High throughput (up to millions of cells); many-dimensional (>40 cellular parameters per cell)

Pros: avoids spectral overlap between fluorophores

Cons: slower flow rate than flow cytometry; expensive; destructive (not possible to sort cells for further analysis)

7

scRNA-seq

Gene expression

Single cells are isolated (for example, through microfluidics, droplet-based methods or flow cytometry-based sorting) and lysed, and their transcripts are captured; the subsequent workflow is similar to that of bulk RNA-seq

High dimensional (>10,000 features measured per cell)

Pros: comprehensive and unbiased sequencing

22

CITE-seqa

Simultaneous surface protein expression and gene expression

Barcoded, oligonucleotide-conjugated antibodies label single cells that are analyzed by scRNA-seq

High dimensional (>100 proteins can be measured per cell in addition to >10,000 genes)

Pros: gene expression integrated with multi-omic profiling

4

scBCR/TCR-seqc

Immune antigen receptor repertoire

Single-cell VDJ-enriched libraries are generated using microfluidics, 5′ molecular barcoding and constant region-specific primers

Paired, full-length receptor sequences from T cells and/or B cells including isotypes

Pros: comprehensive and unbiased sequencing; combination with multi-omic profiling possible (gene and protein expression)

13

  1. scBCR/TCR-seq, scBCR-seq and/or scTCR-seq.
  2. aCITE-seq includes scRNA-seq as part of the workflow; to omit redundancy, we did not count the CITE-seq studies in the scRNA-seq row.
  3. bIncludes spectral flow cytometry (one study), which is based on conventional flow cytometry but uses different optics and detectors.
  4. cscBCR/TCR-seq can also be multi-omic; here we include 12 multi-omic studies that incorporated scBCR/TCR-seq and one scBCR-seq study.
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