Summary of prospective single-cell lineage tracing studies using viral DNA barcoding
| Study | Editing system | Method | Read out | Barcode type | MOI | In vitro or in vivo (species) | Sequencing | Reference |
|---|---|---|---|---|---|---|---|---|
| Zebrafish embryo lineage development | Transposon | TracerSeq | scRNA-seq | GFP + 20 bp | ∼54% of cells with barcode | Zebrafish | InDrops Illumina | Wagner et al. (2018) |
| Lineage-linked cancer transcriptome plasticity | Episome | BdLT-Seq | scRNA-seq | GFP + 12 bp | 0.05 | In vitro | 10 × 3′ | Shlyakhtina et al. (2023) |
| Mouse embryonic fibroblast (MEF) reprogramming | Lentivirus | CellTag | scRNA-seq | GFP + 8 bp | 3–4 | In vitro | Drop-seq, 10 × 3′ | Biddy et al. (2018) |
| Multiple samples with species mixing for sample multiplexing | Lentivirus | CellTag | scRNA-seq snRNA-seq | GFP + 8 bp | 0.5% of cells with barcode | In vitro and mouse | 10 × 3′ | Guo et al. (2019) |
| Nature protocol from Morris | Lentivirus | CellTag | scRNA-seq | GFP + 8 bp | 3–4 | In vitro | 10 × 3′ | Kong et al. (2020) |
| Fate-specific gene regulatory changes in MEF to endoderm transition | Lentivirus | CellTag-multi | scRNA-seq/scATAC-seq | GFP + read 1N + 28 bp + read 2N + RT priming site | ∼2.25 | In vitro | 10x multiome | Jindal et al. (2023) |
| Mouse hematopoietic differentiation | Lentivirus | LARRY | scRNA-seq | GFP + 28 bp | 98% of cells with GFP signal | In vitro and mouse | InDrops Illumina | Weinreb et al. (2020) |
| Mouse brain developmental neurogenesis | Lentivirus | TREX/Space-TREX | scRNA-seq/STa | EGFP + 30 bp | NA | Mouse | 10 × 3′ | Ratz et al. (2022) |
| Stem cell hierarchies in rhabdomyosarcoma | Lentivirus | LARRY | scRNA-seq | GFP + 28 bp | 0.3 | In vitro | 10 × 3′ | Wei et al. (2022) |
| Clonal dynamics in tumor evolution and treatment (CLL) | Lentivirus | ClonMapper | scRNA-seq CROP-seq | sgRNA barcodes with BFP + 20 bp | 0.1 | In vitro | 10 × 3′ | Gutierrez et al. (2021) |
| Cell fate in melanoma drug resistance | Lentivirus | Rewind | RNA FISH | GFP + gDNA (100 bp) | <0.5 | In vitro | Targeted DNA-seq | Emert et al. (2021) |
| Cycling persister cells in lung cancer drug resistance | Lentivirus | Watermelon | scRNA-seq live cell imaging | mNeonGFP + 90 bp (semirandom seq) | 0.3 | In vitro | 10 × 3′ | Oren et al. (2021) |
| Clonal diversity in TNBC primary and metastatic tumors | Lentivirus | Viral barcoding | scRNA-seq | GFP + 98 bp (semirandom seq) | 0.1–0.2 | Mouse | 10 × 3′ | Merino et al. (2019) |
| Malignant clonal fitness in AML | Lentivirus | SPLINTR | scRNA-seq | GFP, BFP or mCherry + 60 bp (semirandom seq) | 0.02–0.1 | In vitro and mouse | 10 × 3′ | Fennell et al. (2022) |
| Mathematical framework to predict cancer therapeutic resistance | Lentivirus | COLBERT | scRNA-seq | BFP + 20 bp gRNA | <0.1 | In vitro | 10 × 3′ | Johnson et al. (2020) |
| Rates, routes and drivers of lung metastasis in xenografts | Lentivirus | Cas9-based recorder | scRNA-seq | BFP + 205 bp triple-gRNAs | ∼0.5 | Mouse | 10 × 3′ | Quinn et al. (2021) |
[i] a(ST) Spatial transcriptomics.