
Barcodes based on nucleic acid sequences: Applications and challenges (Review)
- Authors:
- Ying Hong Wei
- Faquan Lin
-
Affiliations: Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China - Published online on: May 2, 2025 https://doi.org/10.3892/mmr.2025.13552
- Article Number: 187
-
Copyright: © Wei et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
This article is mentioned in:
Abstract
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Loewer A and Lahav G: We are all individuals: Causes and consequences of non-genetic heterogeneity in mammalian cells. Curr Opin Genet Dev. 21:753–758. 2011. View Article : Google Scholar : PubMed/NCBI | |
Wang Y, Zhang X and Wang Z: Cellular barcoding: From developmental tracing to anti-tumor drug discovery. Cancer Lett. 567:2162812023. View Article : Google Scholar : PubMed/NCBI | |
Chen C, Liao Y and Peng G: Connecting past and present: Single-cell lineage tracing. Protein Cell. 13:790–807. 2022. View Article : Google Scholar : PubMed/NCBI | |
Weinreb C and Klein AM: Lineage reconstruction from clonal correlations. Proc Natl Acad Sci USA. 117:17041–17048. 2020. View Article : Google Scholar : PubMed/NCBI | |
De Rop FV, Ismail JN, Bravo González-Blas C, Hulselmans GJ, Flerin CC, Janssens J, Theunis K, Christiaens VM, Wouters J, Marcassa G, et al: HyDrop enables droplet based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads. Elife. 11:e739712022. View Article : Google Scholar : PubMed/NCBI | |
Sulston JE, Schierenberg E, White JG and Thomson JN: The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol. 100:64–119. 1983. View Article : Google Scholar : PubMed/NCBI | |
Lu R, Neff NF, Quake SR and Weissman IL: Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding. Nat Biotechnol. 29:928–933. 2011. View Article : Google Scholar : PubMed/NCBI | |
Weber K, Thomaschewski M, Warlich M, Volz T, Cornils K, Niebuhr B, Täger M, Lütgehetmann M, Pollok JM, Stocking C, et al: RGB marking facilitates multicolor clonal cell tracking. Nat Med. 17:504–509. 2011. View Article : Google Scholar : PubMed/NCBI | |
Weber K, Bartsch U, Stocking C and Fehse B: A multicolor panel of novel lentiviral ‘Gene Ontology’ (LeGO) vectors for functional gene analysis. Mol Ther. 16:698–706. 2008. View Article : Google Scholar : PubMed/NCBI | |
Gomez-Nicola D, Riecken K, Fehse B and Perry VH: In-vivo RGB marking and multicolour single-cell tracking in the adult brain. Sci Rep. 4:75202014. View Article : Google Scholar : PubMed/NCBI | |
Weber K, Mock U, Petrowitz B, Bartsch U and Fehse B: Lentiviral gene ontology (LeGO) vectors equipped with novel drug-selectable fluorescent proteins: New building blocks for cell marking and multi-gene analysis. Gene Ther. 17:511–520. 2010. View Article : Google Scholar : PubMed/NCBI | |
Mohme M, Maire CL, Riecken K, Zapf S, Aranyossy T, Westphal M, Lamszus K and Fehse B: Optical barcoding for single-clone tracking to study tumor heterogeneity. Mol Ther. 25:621–633. 2017. View Article : Google Scholar : PubMed/NCBI | |
Shembrey C, Smith J, Grandin M, Williams N, Cho HJ, Mølck C, Behrenbruch C, Thomson BN, Heriot AG, Merino D and Hollande F: Longitudinal monitoring of intra-tumoural heterogeneity using optical barcoding of patient-derived colorectal tumour models. Cancers (Basel). 14:5812022. View Article : Google Scholar : PubMed/NCBI | |
Schepers K, Swart E, van Heijst JW, Gerlach C, Castrucci M, Sie D, Heimerikx M, Velds A, Kerkhoven RM, Arens R and Schumacher TN: Dissecting T cell lineage relationships by cellular barcoding. J Exp Med. 205:2309–2318. 2008. View Article : Google Scholar : PubMed/NCBI | |
Van Heijst JW, Gerlach C, Swart E, Sie D, Nunes-Alves C, Kerkhoven RM, Arens R, Correia-Neves M, Schepers K and Schumacher TN: Recruitment of antigen-specific CD8+ T cells in response to infection is markedly efficient. Science. 325:1265–1269. 2009. View Article : Google Scholar : PubMed/NCBI | |
Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P and Church GM: Developmental barcoding of whole mouse via homing CRISPR. Science. 361:eaat98042018. View Article : Google Scholar : PubMed/NCBI | |
Kebschull JM and Zador AM: Cellular barcoding: Lineage tracing, screening and beyond. Nat Methods. 15:871–879. 2018. View Article : Google Scholar : PubMed/NCBI | |
Sankaran VG, Weissman JS and Zon LI: Cellular barcoding to decipher clonal dynamics in disease. Science. 378:eabm58742022. View Article : Google Scholar : PubMed/NCBI | |
Serrano A, Berthelet J, Naik SH and Merino D: Mastering the use of cellular barcoding to explore cancer heterogeneity. Nat Rev Cancer. 22:609–624. 2022. View Article : Google Scholar : PubMed/NCBI | |
Merino D, Weber TS, Serrano A, Vaillant F, Liu K, Pal B, Di Stefano L, Schreuder J, Lin D, Chen Y, et al: Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer. Nat Commun. 10:7662019. View Article : Google Scholar : PubMed/NCBI | |
Ko J, Wang Y, Carlson JCT, Marquard A, Gungabeesoon J, Charest A, Weitz D, Pittet MJ and Weissleder R: Single extracellular vesicle protein analysis using immuno-droplet digital polymerase chain reaction amplification. Adv Biosyst. 4:e19003072020. View Article : Google Scholar : PubMed/NCBI | |
Banijamali M, Höjer P, Nagy A, Hååg P, Gomero EP, Stiller C, Kaminskyy VO, Ekman S, Lewensohn R, Karlström AE, et al: Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis. J Extracell Vesicles. 11:e122772022. View Article : Google Scholar : PubMed/NCBI | |
Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK and Sherwood RI: A multiplexed barcodelet single-cell RNA-Seq approach elucidates combinatorial signaling pathways that drive ESC differentiation. Cell Stem Cell. 26:938–950.e6. 2020. View Article : Google Scholar : PubMed/NCBI | |
Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA and Kirschner MW: Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 161:1187–1201. 2015. View Article : Google Scholar : PubMed/NCBI | |
Perié L, Duffy KR, Kok L, de Boer RJ and Schumacher TN: The branching point in erythro-myeloid differentiation. Cell. 163:1655–1662. 2015. View Article : Google Scholar : PubMed/NCBI | |
Schueder F, Unterauer EM, Ganji M and Jungmann R: DNA-Barcoded fluorescence microscopy for spatial omics. Proteomics. 20:e19003682020. View Article : Google Scholar : PubMed/NCBI | |
Howland KK and Brock A: Cellular barcoding tracks heterogeneous clones through selective pressures and phenotypic transitions. Trends Cancer. 9:591–601. 2023. View Article : Google Scholar : PubMed/NCBI | |
Kretzschmar K and Watt FM: Lineage Tracing. Cell. 148:33–45. 2012. View Article : Google Scholar : PubMed/NCBI | |
Perié L and Duffy KR: Retracing the in vivo haematopoietic tree using single-cell methods. FEBS Lett. 590:4068–4083. 2016. View Article : Google Scholar : PubMed/NCBI | |
Kok L, Masopust D and Schumacher TN: The precursors of CD8+ tissue resident memory T cells: From lymphoid organs to infected tissues. Nat Rev Immunol. 22:283–293. 2022. View Article : Google Scholar : PubMed/NCBI | |
Naik SH, Perié L, Swart E, Gerlach C, van Rooij N, de Boer RJ and Schumacher TN: Diverse and heritable lineage imprinting of early haematopoietic progenitors. Nature. 496:229–232. 2013. View Article : Google Scholar : PubMed/NCBI | |
Dhimolea E, De Matos Simoes R, Kansara D, Al'Khafaji A, Bouyssou J, Weng X, Sharma S, Raja J, Awate P, Shirasaki R, et al: An embryonic diapause-like adaptation with suppressed myc activity enables tumor treatment persistence. Cancer Cell. 39:240–256.e11. 2021. View Article : Google Scholar : PubMed/NCBI | |
Echeverria GV, Ge Z, Seth S, Zhang X, Jeter-Jones S, Zhou X, Cai S, Tu Y, McCoy A, Peoples M, et al: Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Sci Transl Med. 11:eaav09362019. View Article : Google Scholar : PubMed/NCBI | |
Echeverria GV, Powell E, Seth S, Ge Z, Carugo A, Bristow C, Peoples M, Robinson F, Qiu H, Shao J, et al: High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer. Nat Commun. 9:50792018. View Article : Google Scholar : PubMed/NCBI | |
Blundell JR and Levy SF: Beyond genome sequencing: Lineage tracking with barcodes to study the dynamics of evolution, infection, and cancer. Genomics. 104((6 Pt A)): 417–430. 2014. View Article : Google Scholar : PubMed/NCBI | |
Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, et al: Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 161:1202–1214. 2015. View Article : Google Scholar : PubMed/NCBI | |
Naik SH, Schumacher TN and Perié L: Cellular barcoding: A technical appraisal. Exp Hematol. 42:598–608. 2014. View Article : Google Scholar : PubMed/NCBI | |
Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N and Junker JP: Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol. 36:469–473. 2018. View Article : Google Scholar : PubMed/NCBI | |
Wagner DE and Klein AM: Lineage tracing meets single-cell omics: opportunities and challenges. Nat Rev Genet. 21:410–427. 2020. View Article : Google Scholar : PubMed/NCBI | |
Cai D, Cohen KB, Luo T, Lichtman JW and Sanes JR: Improved tools for the Brainbow toolbox. Nat Methods. 10:540–547. 2013. View Article : Google Scholar | |
Pei W, Feyerabend TB, Rössler J, Wang X, Postrach D, Busch K, Rode I, Klapproth K, Dietlein N, Quedenau C, et al: Polylox barcoding reveals haematopoietic stem cell fates realized in vivo. Nature. 548:456–460. 2017. View Article : Google Scholar : PubMed/NCBI | |
Pei W, Wang X, Rössler J, Feyerabend TB, Höfer T and Rodewald HR: Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc. 14:1820–1840. 2019. View Article : Google Scholar : PubMed/NCBI | |
McLellan MA, Rosenthal NA and Pinto AR: Cre- loxP-mediated recombination: General principles and experimental considerations. Curr Protoc Mouse Biol. 7:1–12. 2017. View Article : Google Scholar : PubMed/NCBI | |
Pei W, Shang F, Wang X, Fanti AK, Greco A, Busch K, Klapproth K, Zhang Q, Quedenau C, Sauer S, et al: Resolving fates and single-cell transcriptomes of hematopoietic stem cell clones by polyloxexpress barcoding. Cell Stem Cell. 27:383–395.e8. 2020. View Article : Google Scholar : PubMed/NCBI | |
Becher B, Waisman A and Lu LF: Conditional gene-targeting in mice: Problems and solutions. Immunity. 48:835–836. 2018. View Article : Google Scholar : PubMed/NCBI | |
McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M and Gottardo R: Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics. 29:461–467. 2013. View Article : Google Scholar : PubMed/NCBI | |
Kharchenko PV, Silberstein L and Scadden DT: Bayesian approach to single-cell differential expression analysis. Nat Methods. 11:740–742. 2014. View Article : Google Scholar : PubMed/NCBI | |
Fan J, Slowikowski K and Zhang F: Single-cell transcriptomics in cancer: Computational challenges and opportunities. Exp Mol Med. 52:1452–1465. 2020. View Article : Google Scholar : PubMed/NCBI | |
Lu T, Park S, Zhu J, Wang Y, Zhan X, Wang X, Wang L, Zhu H and Wang T: Overcoming expressional drop-outs in lineage reconstruction from single-cell RNA-sequencing data. Cell Rep. 34:1085892021. View Article : Google Scholar : PubMed/NCBI | |
Wang JY and Doudna JA: CRISPR technology: A decade of genome editing is only the beginning. Science. 379:eadd86432023. View Article : Google Scholar : PubMed/NCBI | |
Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA and Schier AF: Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol. 36:442–450. 2018. View Article : Google Scholar : PubMed/NCBI | |
McKenna A, Findlay GM, Gagnon JA, Horwitz MS, Schier AF and Shendure J: Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science. 353:aaf79072016. View Article : Google Scholar : PubMed/NCBI | |
Raj B, Gagnon JA and Schier AF: Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. Nat Protoc. 13:2685–2713. 2018. View Article : Google Scholar : PubMed/NCBI | |
Simeonov KP, Byrns CN, Clark ML, Norgard RJ, Martin B, Stanger BZ, Shendure J, McKenna A and Lengner CJ: Single-cell lineage tracing of metastatic cancer reveals selection of hybrid EMT states. Cancer Cell. 39:1150–1162.e9. 2021. View Article : Google Scholar : PubMed/NCBI | |
Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan WC, Fujiwara Y, Li BE, et al: An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells. Cell. 181:1410–1422.e27. 2020. View Article : Google Scholar : PubMed/NCBI | |
Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, Jost M, Quinn JJ, Yang D, Jones MG, et al: Molecular recording of mammalian embryogenesis. Nature. 570:77–82. 2019. View Article : Google Scholar : PubMed/NCBI | |
Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, Bivona TG and Weissman JS: Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science (New York, NY). 371:eabc19442021. View Article : Google Scholar | |
Yang D, Jones MG, Naranjo S, Rideout WM III, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, et al: Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell. 185:1905–1923.e25. 2022. View Article : Google Scholar : PubMed/NCBI | |
Xie L, Liu H, You Z, Wang L, Li Y, Zhang X, Ji X, He H, Yuan T, Zheng W, et al: Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding. Nat Methods. 20:1244–1255. 2023. View Article : Google Scholar : PubMed/NCBI | |
Alemany A, Florescu M, Baron CS, Peterson-Maduro J and Van Oudenaarden A: Whole-organism clone tracing using single-cell sequencing. Nature. 556:108–112. 2018. View Article : Google Scholar : PubMed/NCBI | |
Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Páleníková P, Khodak A, Kiselev V, Kosicki M, et al: Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol. Nov 27–2018.(Epub ahead of print). | |
Schmidt ST, Zimmerman SM, Wang J, Kim SK and Quake SR: Quantitative analysis of synthetic cell lineage tracing using nuclease barcoding. ACS Synth Biol. 6:936–942. 2017. View Article : Google Scholar : PubMed/NCBI | |
Varanasi A and Wilson E: The Applications of the CRISPR/Cas9 Gene-Editing System in Treating Human Diseases. J Stud Res. 11:1–17. 2022. View Article : Google Scholar | |
Choubisa V and Sharma V: Unveiling neural network potential in forecasting CRISPR effects and off-target prophecies for gene editing. Int J Sci Res Arch. 10:252–259. 2023. View Article : Google Scholar | |
Moreno-Ayala R and Junker JP: Single-cell genomics to study developmental cell fate decisions in zebrafish. Brief Funct Genomics. Mar 30–2021.(Epub ahead of print). View Article : Google Scholar : PubMed/NCBI | |
Yabe IM, Truitt LL, Espinoza DA, Wu C, Koelle S, Panch S, Corat MAF, Winkler T, Yu KR, Hong SG, et al: Barcoding of macaque hematopoietic stem and progenitor cells: A robust platform to assess vector genotoxicity. Mol Ther Methods Clin Dev. 11:143–154. 2018. View Article : Google Scholar : PubMed/NCBI | |
Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, et al: NmeCas9 is an intrinsically high-fidelity genome-editing platform. Genome Biol. 19:2142018. View Article : Google Scholar : PubMed/NCBI | |
Zhao L, Liu Z, Levy SF and Wu S: Bartender: A fast and accurate clustering algorithm to count barcode reads. Bioinformatics. 34:739–747. 2018. View Article : Google Scholar : PubMed/NCBI | |
Johnson MS, Venkataram S and Kryazhimskiy S: Best practices in designing, sequencing, and identifying random DNA barcodes. J Mol Evol. 91:263–280. 2023. View Article : Google Scholar : PubMed/NCBI | |
Störtz F and Minary P: crisprSQL: A novel database platform for CRISPR/Cas off-target cleavage assays. Nucleic Acids Res. 49((D1)): D855–D861. 2021. View Article : Google Scholar : PubMed/NCBI | |
Cradick TJ, Qiu P, Lee CM, Fine EJ and Bao G: COSMID: A web-based tool for identifying and validating CRISPR/Cas off-target sites. Mol Ther Nucleic Acids. 3:e2142014. View Article : Google Scholar : PubMed/NCBI | |
Bystrykh LV and Belderbos ME: Clonal analysis of cells with cellular barcoding: When numbers and sizes matter. Methods Mol Biol. 1516:57–89. 2016. View Article : Google Scholar : PubMed/NCBI | |
Rodriguez-Fraticelli AE, Wolock SL, Weinreb CS, Panero R, Patel SH, Jankovic M, Sun J, Calogero RA, Klein AM and Camargo FD: Clonal analysis of lineage fate in native haematopoiesis. Nature. 553:212–216. 2018. View Article : Google Scholar : PubMed/NCBI | |
Bramlett C, Jiang D, Nogalska A, Eerdeng J, Contreras J and Lu R: Clonal tracking using embedded viral barcoding and high-throughput sequencing. Nat Protoc. 15:1436–1458. 2020. View Article : Google Scholar : PubMed/NCBI | |
Ordon J, Thouin J, Nakano RT, et al: Simultaneous tracking of near-isogenic bacterial strains in synthetic Arabidopsis microbiota by chromosomally-integrated barcodes. 2023. | |
Leibovich N and Goyal S: Limitations and Optimizations of Cellular Lineages Tracking. biorxiv. doi:. https://doi.org/10.1101/2023.03.15.532767 | |
Frenkel M, Hujoel MLA, Morris Z and Raman S: Discovering chromatin dysregulation induced by protein-coding perturbations at scale. bioRxiv. doi:. https://doi.org/10.1101/2023.09.20.555752 | |
Blois S, Goetz BM, Bull JJ and Sullivan CS: Interpreting and de-noising genetically engineered barcodes in a DNA virus. PLoS Comput Biol. 18:e10101312022. View Article : Google Scholar : PubMed/NCBI | |
Anwar SL, Wulaningsih W and Lehmann U: Transposable elements in human cancer: Causes and consequences of deregulation. Int J Mol Sci. 18:9742017. View Article : Google Scholar : PubMed/NCBI | |
Ohigashi I, Yamasaki Y, Hirashima T and Takahama Y: Identification of the transgenic integration site in immunodeficient tgε26 human CD3ε transgenic mice. PLoS One. 5:e143912010. View Article : Google Scholar : PubMed/NCBI | |
Wolff JH and Mikkelsen JG: Delivering genes with human immunodeficiency virus-derived vehicles: Still state-of-the-art after 25 years. J Biomed Sci. 29:792022. View Article : Google Scholar : PubMed/NCBI | |
Porter SN, Baker LC, Mittelman D and Porteus MH: Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo. Genome Biol. 15:R752014. View Article : Google Scholar : PubMed/NCBI | |
Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S and Taipale J: Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 9:72–74. 2012. View Article : Google Scholar : PubMed/NCBI | |
Fan HC, Fu GK and Fodor SP: Combinatorial labeling of single cells for gene expression cytometry. Science. 347:12583672015. View Article : Google Scholar : PubMed/NCBI | |
Hashimshony T, Wagner F, Sher N and Yanai I: CEL-Seq: Single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2:666–673. 2012. View Article : Google Scholar : PubMed/NCBI | |
Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G and Sandberg R: Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods. 10:1096–1098. 2013. View Article : Google Scholar : PubMed/NCBI | |
Zhang X, Li T, Liu F, Chen Y, Yao J, Li Z, Huang Y and Wang J: Comparative analysis of droplet-based ultra-high-throughput single-cell RNA-Seq systems. Mol Cell. 73:130–142.e5. 2019. View Article : Google Scholar : PubMed/NCBI | |
Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, et al: Massively parallel digital transcriptional profiling of single cells. Nat Commun. 8:140492017. View Article : Google Scholar : PubMed/NCBI | |
Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE and Weitz DA: High-throughput single-cell labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics. PLoS One. 10:e01163282015. View Article : Google Scholar : PubMed/NCBI | |
Pinglay S, Lalanne JB, Daza RM, Koeppel J, Li X, Lee DS and Shendure J: Multiplex generation and single-cell analysis of structural variants in mammalian genomes. Science. 387:eado59782025. View Article : Google Scholar : PubMed/NCBI | |
Lan F, Demaree B, Ahmed N and Abate AR: Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat Biotechnol. 35:640–646. 2017. View Article : Google Scholar : PubMed/NCBI | |
Li J, Zhang R, Li T, et al: Ultra-high-throughput microbial single-cell whole genome sequencing for genome-resolved metagenomics. 2022. View Article : Google Scholar | |
Shembekar N, Chaipan C, Utharala R and Merten CA: Droplet-based microfluidics in drug discovery, transcriptomics and high-throughput molecular genetics. Lab Chip. 16:1314–1331. 2016. View Article : Google Scholar : PubMed/NCBI | |
Suea-Ngam A, Howes PD, Srisa-Art M and deMello AJ: Droplet microfluidics: From proof-of-concept to real-world utility? Chem Commun (Camb). 55:9895–9903. 2019. View Article : Google Scholar : PubMed/NCBI | |
Sheng C, Lopes R, Li G, et al: Probabilistic machine learning ensures accurate ambient denoising in droplet-based single-cell omics. 2022. View Article : Google Scholar | |
Imoto Y: Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform. biorxiv. doi:. https://doi.org/10.1101/2024.04.18.590054 | |
Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH; Brain Somatic Mosaicism Network, ; Weinberger DR, Moran JV, Kidd JM, et al: Mapping recurrent mosaic copy number variation in human neurons. Nat Commun. 15:42202024. View Article : Google Scholar : PubMed/NCBI | |
Bo L, Liang Y and Lin G: Cancer classification based on multiple dimensions: SNV patterns. Comput Biol Med. 151((Pt A)): 1062702022.PubMed/NCBI | |
McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM and Gage FH: Mosaic copy number variation in human neurons. Science. 342:632–637. 2013. View Article : Google Scholar : PubMed/NCBI | |
Addis L, Ahn JW, Dobson R, Dixit A, Ogilvie CM, Pinto D, Vaags AK, Coon H, Chaste P, Wilson S, et al: Microdeletions of ELP4 are associated with language impairment, autism spectrum disorder, and mental retardation. Hum Mutat. 36:842–850. 2015. View Article : Google Scholar : PubMed/NCBI | |
Xiong E, Liu P, Deng R, Zhang K, Yang R and Li J: Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro. Natl Sci Rev. 11:nwae1182024. View Article : Google Scholar : PubMed/NCBI | |
Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D and Eberwine J: Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons. BMC Biol. 22:1622024. View Article : Google Scholar : PubMed/NCBI | |
Dondi A, Borgsmüller N, Ferreira PF, Haas BJ, Jacob F and Heinzelmann-Schwarz V; Tumor Profiler Consortium; Beerenwinkel N, : De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. bioRxiv [Preprint]. 2024.03.06.583775. 2024. | |
Ganz J, Luquette LJ, Bizzotto S, Miller MB, Zhou Z, Bohrson CL, Jin H, Tran AV, Viswanadham VV, McDonough G, et al: Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes. Cell. 187:1955–1970.e23. 2024. View Article : Google Scholar : PubMed/NCBI | |
Csordas A, Sipos B, Kurucova T, Volfova A, Zamola F, Tichy B and Hicks DG: Cell Tree Rings: The structure of somatic evolution as a human aging timer. Geroscience. 46:3005–3019. 2024. View Article : Google Scholar : PubMed/NCBI | |
You X, Cao Y, Suzuki T, Shao J, Zhu B, Masumura K, Xi J, Liu W, Zhang X and Luan Y: Genome-wide direct quantification of in vivo mutagenesis using high-accuracy paired-end and complementary consensus sequencing. Nucleic Acids Res. 51:e1092023. View Article : Google Scholar : PubMed/NCBI | |
Weng C, Weissman JS and Sankaran VG: Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling. bioRxiv [Preprint]. 2024.08.23.609473. 2024. | |
Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ and Walsh CA: Cell lineage analysis in human brain using endogenous retroelements. Neuron. 85:49–59. 2015. View Article : Google Scholar : PubMed/NCBI | |
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al: Global variation in copy number in the human genome. Nature. 444:444–454. 2006. View Article : Google Scholar : PubMed/NCBI | |
Wei CJ and Zhang K: RETrace: Simultaneous retrospective lineage tracing and methylation profiling of single cells. Genome Res. 30:602–610. 2020. View Article : Google Scholar : PubMed/NCBI | |
Fink J, Andersson-Rolf A and Koo BK: Adult stem cell lineage tracing and deep tissue imaging. BMB Rep. 48:655–667. 2015. View Article : Google Scholar : PubMed/NCBI | |
Woodworth MB, Girskis KM and Walsh CA: Building a lineage from single cells: Genetic techniques for cell lineage tracking. Nat Rev Genet. 18:230–244. 2017. View Article : Google Scholar : PubMed/NCBI | |
Li L, Bowling S, McGeary SE, Yu Q, Lemke B, Alcedo K, Jia Y, Liu X, Ferreira M, Klein AM, et al: A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell. 186:5183–5199.e22. 2023. View Article : Google Scholar : PubMed/NCBI | |
Walsh C and Cepko CL: Widespread dispersion of neuronal clones across functional regions of the cerebral cortex. Science. 255:434–440. 1992. View Article : Google Scholar : PubMed/NCBI | |
Gerrits A, Dykstra B, Kalmykowa OJ, Klauke K, Verovskaya E, Broekhuis MJ, de Haan G and Bystrykh LV: Cellular barcoding tool for clonal analysis in the hematopoietic system. Blood. 115:2610–2618. 2010. View Article : Google Scholar : PubMed/NCBI | |
Golden JA, Fields-Berry SC and Cepko CL: Construction and characterization of a highly complex retroviral library for lineage analysis. Proc Natl Acad Sci USA. 92:5704–5708. 1995. View Article : Google Scholar : PubMed/NCBI | |
Khozyainova AA, Valyaeva AA, Arbatsky MS, Isaev SV, Iamshchikov PS, Volchkov EV, Sabirov MS, Zainullina VR, Chechekhin VI, Vorobev RS, et al: Complex analysis of single-cell RNA sequencing data. Biochemistry (Mosc). 88:231–252. 2023. View Article : Google Scholar : PubMed/NCBI | |
Weinreb C, Rodriguez-Fraticelli A, Camargo FD and Klein AM: Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science. 367:eaaw33812020. View Article : Google Scholar : PubMed/NCBI | |
Bizzotto S, Dou Y, Ganz J, Doan RN, Kwon M, Bohrson CL, Kim SN, Bae T, Abyzov A; NIMH Brain Somatic Mosaicism Network, ; et al: Landmarks of human embryonic development inscribed in somatic mutations. Science. 371:1249–1253. 2021. View Article : Google Scholar : PubMed/NCBI | |
Sun J, Ramos A, Chapman B, Johnnidis JB, Le L, Ho YJ, Klein A, Hofmann O and Camargo FD: Clonal dynamics of native haematopoiesis. Nature. 514:322–327. 2014. View Article : Google Scholar : PubMed/NCBI | |
Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L and Bernstein BE: Parallel single-cell RNA-Seq and genetic recording reveals lineage decisions in developing embryoid bodies. Cell Rep. 33:1082222020. View Article : Google Scholar : PubMed/NCBI | |
Wagenblast E, Soto M, Gutiérrez-Ángel S, Hartl CA, Gable AL, Maceli AR, Erard N, Williams AM, Kim SY, Dickopf S, et al: A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis. Nature. 520:358–362. 2015. View Article : Google Scholar : PubMed/NCBI | |
Akimov Y, Bulanova D, Timonen S, Wennerberg K and Aittokallio T: Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics. Mol Syst Biol. 16:e91952020. View Article : Google Scholar : PubMed/NCBI | |
McKenna A and Gagnon JA: Recording development with single cell dynamic lineage tracing. Development. 146:dev1697302019. View Article : Google Scholar : PubMed/NCBI | |
Wang MY, Zhou Y, Lai GS, Huang Q, Cai WQ, Han ZW, Wang Y, Ma Z, Wang XW, Xiang Y, et al: DNA barcode to trace the development and differentiation of cord blood stem cells (Review). Mol Med Rep. 24:8492021. View Article : Google Scholar : PubMed/NCBI | |
Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, Codeluppi S, Plaza Reyes A, Linnarsson S, Sandberg R and Lanner F: Single-cell RNA-Seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell. 165:1012–1026. 2016. View Article : Google Scholar : PubMed/NCBI | |
Farrell JA, Wang Y, Riesenfeld SJ, Shekhar K, Regev A and Schier AF: Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science. 360:eaar31312018. View Article : Google Scholar : PubMed/NCBI | |
McFarland JM, Paolella BR, Warren A, Geiger-Schuller K, Shibue T, Rothberg M, Kuksenko O, Colgan WN, Jones A, Chambers E, et al: Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Nat Commun. 11:42962020. View Article : Google Scholar : PubMed/NCBI | |
Birnbaum KD: Power in numbers: Single-cell RNA-Seq strategies to dissect complex tissues. Annu Rev Genet. 52:203–221. 2018. View Article : Google Scholar : PubMed/NCBI | |
Lan F, Saba J, Ross TD, Zhou Z, Krauska K, Anantharaman K, Landick R and Venturelli OS: Massively parallel single-cell sequencing of diverse microbial populations. Nat Methods. 21:228–235. 2024. View Article : Google Scholar : PubMed/NCBI | |
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, Steemers FJ, Trapnell C and Shendure J: Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 348:910–914. 2015. View Article : Google Scholar : PubMed/NCBI | |
Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, Lucero J, Behrens MM, Hu M and Ren B: An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat Struct Mol Biol. 26:1063–1070. 2019. View Article : Google Scholar : PubMed/NCBI | |
Wu B, Bennett HM, Ye X, Sridhar A, Eidenschenk C, Everett C, Nazarova EV, Chen HH, Kim IK, Deangelis M, et al: Overloading And unpacKing (OAK)-droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling. Nat Commun. 15:91462024. View Article : Google Scholar : PubMed/NCBI | |
Mathur L, Szalai B, Du NH, Utharala R, Ballinger M, Landry JJM, Ryckelynck M, Benes V, Saez-Rodriguez J and Merten CA: Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets. Nat Commun. 13:44502022. View Article : Google Scholar : PubMed/NCBI | |
Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, et al: A resource for large-scale RNA-interference-based screens in mammals. Nature. 428:427–431. 2004. View Article : Google Scholar : PubMed/NCBI | |
Silva JM, Marran K, Parker JS, Silva J, Golding M, Schlabach MR, Elledge SJ, Hannon GJ and Chang K: Profiling essential genes in human mammary cells by multiplex RNAi screening. Science. 319:617–620. 2008. View Article : Google Scholar : PubMed/NCBI | |
Datlinger P, Rendeiro AF, Schmidl C, Krausgruber T, Traxler P, Klughammer J, Schuster LC, Kuchler A, Alpar D and Bock C: Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods. 14:297–301. 2017. View Article : Google Scholar : PubMed/NCBI | |
Duncombe TA and Dittrich PS: Droplet barcoding: Tracking mobile micro-reactors for high-throughput biology. Curr Opin Biotechnol. 60:205–212. 2019. View Article : Google Scholar : PubMed/NCBI | |
Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, Villalta JE, Gilbert LA, Horlbeck MA, Hein MY, et al: A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Cell. 167:1867–1882.e21. 2016. View Article : Google Scholar : PubMed/NCBI | |
Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A and Amit I: Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell. 167:1883–1896.e15. 2016. View Article : Google Scholar : PubMed/NCBI | |
Emanuel G, Moffitt JR and Zhuang X: High-throughput, image-based screening of pooled genetic-variant libraries. Nat Methods. 14:1159–1162. 2017. View Article : Google Scholar : PubMed/NCBI | |
Camp JG, Platt R and Treutlein B: Mapping human cell phenotypes to genotypes with single-cell genomics. Science. 365:1401–1405. 2019. View Article : Google Scholar : PubMed/NCBI | |
Xie S, Duan J, Li B, Zhou P and Hon GC: Multiplexed engineering and analysis of combinatorial enhancer activity in single cells. Mol Cell. 66:285–299.e5. 2017. View Article : Google Scholar : PubMed/NCBI | |
Lawson MJ, Camsund D, Larsson J, Baltekin Ö, Fange D and Elf J: In situ genotyping of a pooled strain library after characterizing complex phenotypes. Mol Syst Biol. 13:9472017. View Article : Google Scholar : PubMed/NCBI | |
Marusyk A, Janiszewska M and Polyak K: Intratumor heterogeneity: The rosetta stone of therapy resistance. Cancer Cell. 37:471–484. 2020. View Article : Google Scholar : PubMed/NCBI | |
Shembrey C, Huntington ND and Hollande F: Impact of tumor and immunological heterogeneity on the anti-cancer immune response. Cancers (Basel). 11:12172019. View Article : Google Scholar : PubMed/NCBI | |
Lewis SM, Asselin-Labat ML, Nguyen Q, Berthelet J, Tan X, Wimmer VC, Merino D, Rogers KL and Naik SH: Spatial omics and multiplexed imaging to explore cancer biology. Nat Methods. 18:997–1012. 2021. View Article : Google Scholar : PubMed/NCBI | |
Fennell KA, Vassiliadis D, Lam EYN, Martelotto LG, Balic JJ, Hollizeck S, Weber TS, Semple T, Wang Q, Miles DC, et al: Non-genetic determinants of malignant clonal fitness at single-cell resolution. Nature. 601:125–131. 2022. View Article : Google Scholar : PubMed/NCBI | |
Jin X, Demere Z, Nair K, Ali A, Ferraro GB, Natoli T, Deik A, Petronio L, Tang AA, Zhu C, et al: A metastasis map of human cancer cell lines. Nature. 588:331–336. 2020. View Article : Google Scholar : PubMed/NCBI | |
Holcar M, Ferdin J, Sitar S, Tušek-Žnidarič M, Dolžan V, Plemenitaš A, Žagar E and Lenassi M: Enrichment of plasma extracellular vesicles for reliable quantification of their size and concentration for biomarker discovery. Sci Rep. 10:213462020. View Article : Google Scholar : PubMed/NCBI | |
Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, et al: Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles. 13:e124042024. View Article : Google Scholar : PubMed/NCBI | |
Lozano-Andrés E, Enciso-Martinez A, Gijsbers A, Ridolfi A, Van Niel G, Libregts SFWM, Pinheiro C, van Herwijnen MJC, Hendrix A, Brucale M, et al: Physical association of low density lipoprotein particles and extracellular vesicles unveiled by single particle analysis. J Extracell Vesicles. 12:e123762023. View Article : Google Scholar : PubMed/NCBI | |
Chang W-H, Cerione RA and Antonyak MA: Extracellular Vesicles and Their Roles in Cancer Progression. Cancer Cell Signaling. vol. 2174. Robles-Flores M: Springer US; New York, NY: pp. 143–170. 2021, View Article : Google Scholar | |
Ferguson S, Yang KS and Weissleder R: Single extracellular vesicle analysis for early cancer detection. Trends Mol Med. 28:681–692. 2022. View Article : Google Scholar : PubMed/NCBI | |
Yu W, Hurley J, Roberts D, Chakrabortty SK, Enderle D, Noerholm M, Breakefield XO and Skog JK: Exosome-based liquid biopsies in cancer: opportunities and challenges. Ann Oncol. 32:466–477. 2021. View Article : Google Scholar : PubMed/NCBI | |
Verweij FJ, Balaj L, Boulanger CM, Carter DRF, Compeer EB, D'Angelo G, El Andaloussi S, Goetz JG, Gross JC, Hyenne V, et al: The power of imaging to understand extracellular vesicle biology in vivo. Nat Methods. 18:1013–1026. 2021. View Article : Google Scholar : PubMed/NCBI | |
Crescitelli R, Lässer C and Lötvall J: Isolation and characterization of extracellular vesicle subpopulations from tissues. Nat Protoc. 16:1548–1580. 2021. View Article : Google Scholar : PubMed/NCBI | |
Ko J, Wang Y, Sheng K, Weitz DA and Weissleder R: Sequencing-based protein analysis of single extracellular vesicles. ACS Nano. 15:5631–5638. 2021. View Article : Google Scholar : PubMed/NCBI | |
Ivanova A, Chalupska R, Louro AF, Firth M, González-King Garibotti H, Hultin L, Kohl F, Lázaro-Ibáñez E, Lindgren J, Musa G, et al: Barcoded hybrids of extracellular vesicles and lipid nanoparticles for multiplexed analysis of tissue distribution. Adv Sci (Weinh). 12:e24078502025. View Article : Google Scholar : PubMed/NCBI | |
Kunitake K, Mizuno T, Hattori K, Oneyama C, Kamiya M, Ota S, Urano Y and Kojima R: Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis and release regulators. Nat Commun. 15:97772024. View Article : Google Scholar : PubMed/NCBI | |
Farzad N, Enninful A, Bao S, Zhang D, Deng Y and Fan R: Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nat Protoc. 19:3389–3425. 2024. View Article : Google Scholar : PubMed/NCBI | |
Pandit S, Duchow M, Chao W, Capasso A and Samanta D: DNA-barcoded plasmonic nanostructures for activity-based protease sensing. Angew Chem Int Ed Engl. 63:e2023109642024. View Article : Google Scholar : PubMed/NCBI | |
Lareau CA, Ma S, Duarte FM and Buenrostro JD: Inference and effects of barcode multiplets in droplet-based single-cell assays. Nat Commun. 11:8662020. View Article : Google Scholar : PubMed/NCBI | |
Hotinger JA, Campbell IW, Hullahalli K, Osaki A and Waldor MK: Quantification of Salmonella enterica serovar typhimurium population dynamics in murine infection using a highly diverse barcoded library. Elife. 13:RP1013882024. View Article : Google Scholar | |
Karlsson F, Kallas T, Thiagarajan D, Karlsson M, Schweitzer M, Navarro JF, Leijonancker L, Geny S, Pettersson E, Rhomberg-Kauert J, et al: Molecular pixelation: spatial proteomics of single cells by sequencing. Nat Methods. 21:1044–1052. 2024. View Article : Google Scholar : PubMed/NCBI | |
Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P and Bernstein BE: Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol. 21:1742020. View Article : Google Scholar : PubMed/NCBI | |
Maetzig T, Morgan M and Schambach A: Fluorescent genetic barcoding for cellular multiplex analyses. Exp Hematol. 67:10–17. 2018. View Article : Google Scholar : PubMed/NCBI | |
Maetzig T, Ruschmann J, Sanchez Milde L, Lai CK, Von Krosigk N and Humphries RK: Lentiviral Fluorescent Genetic Barcoding for Multiplex Fate Tracking of Leukemic Cells. Mol Ther Methods Clin Dev. 6:54–65. 2017. View Article : Google Scholar : PubMed/NCBI | |
Yoon B, Kim H, Jung SW and Park J: Single-cell lineage tracing approaches to track kidney cell development and maintenance. Kidney Int. 105:1186–1199. 2024. View Article : Google Scholar : PubMed/NCBI |