Regev, A. et al. The Human Cell Atlas. eLife 6, e27041–e27041 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Kolodziejczyk, A. A., Kim, J. K., Svensson, V., Marioni, J. C. & Teichmann, S. A. The technology and biology of single-cell RNA sequencing. Mol. Cell 58, 610–620 (2015).

Article  CAS  PubMed  Google Scholar 

Grün, D. & van Oudenaarden, A. Design and analysis of single-cell sequencing experiments. Cell 163, 799–810 (2015).

Article  PubMed  Google Scholar 

Elmentaite, R., Domínguez Conde, C., Yang, L. & Teichmann, S. A. Single-cell atlases: shared and tissue-specific cell types across human organs. Nat. Rev. Genet. 23, 395–410 (2022).

Article  CAS  PubMed  Google Scholar 

Wen, L. & Tang, F. Recent advances in single-cell sequencing technologies. Precis. Clin. Med. 5, pbac002 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Macaulay, I. C. et al. Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat. Protoc. 11, 2081–2103 (2016).

Article  CAS  PubMed  Google Scholar 

Macaulay, I. C. et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519–522 (2015). This paper presents one of the first demonstrations of physically separating DNA and poly(A) RNA from a single cell for whole-genome sequencing and full-length transcript sequencing.

Article  CAS  PubMed  Google Scholar 

Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).

Article  CAS  PubMed  Google Scholar 

Li, W., Calder, R. B., Mar, J. C. & Vijg, J. Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Mutat. Res. Mol. Mech. Mutagen. 772, 55–62 (2015).

Article  CAS  Google Scholar 

Macaulay, I. C. & Voet, T. Single cell genomics: advances and future perspectives. PLoS Genet. 10, e1004126 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Gawad, C., Koh, W. & Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175–188 (2016).

Article  CAS  PubMed  Google Scholar 

Svensson, V., Vento-Tormo, R. & Teichmann, S. A. Exponential scaling of single-cell RNA-seq in the past decade. Nat. Protoc. 13, 599–604 (2018).

Article  CAS  PubMed  Google Scholar 

Han, K. Y. et al. SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells. Genome Res. 28, 75–87 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zachariadis, V., Cheng, H., Andrews, N. & Enge, M. A highly scalable method for joint whole-genome sequencing and gene-expression profiling of single cells. Mol. Cell 80, 541–553.e5 (2020). This paper presents the feasibility of separating cytoplasmic RNA from nuclear DNA, enabling separate RNA-seq and DNA-seq library construction through direct tagmentation of the DNA, thus avoiding upfront WGA.

Article  CAS  PubMed  Google Scholar 

Valecha, M. & Posada, D. Somatic variant calling from single-cell DNA sequencing data. Comput. Struct. Biotechnol. J. 20, 2978–2985 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Han, L. et al. Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform. Sci. Rep. 4, 6485 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

van Strijp, D. et al. Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell. Sci. Rep. 7, 11030 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Dey, S. S., Kester, L., Spanjaard, B., Bienko, M. & van Oudenaarden, A. Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 33, 285–289 (2015). This paper presents one of the first demonstrations of joint preamplification of single-cell gDNA and poly(A) RNA-derived cDNA, followed by splitting of the reaction for DNA-seq and RNA-seq library preparation.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rodriguez-Meira, A. et al. Unravelling intratumoral heterogeneity through high-sensitivity single-cell mutational analysis and parallel RNA sequencing. Mol. Cell 73, 1292–1305.e8 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yu, L. et al. scONE-seq: a single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors. Sci. Adv. 9, eabp8901 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yin, Y. et al. High-throughput single-cell sequencing with linear amplification. Mol. Cell 76, 676–690.e10 (2019). This paper presents one of the first demonstrations of combinatorial indexing for joint single-cell DNA and RNA sequencing, enabling massive throughput.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rambow, F. et al. Toward minimal residual disease-directed therapy in melanoma. Cell 174, 843–855.e19 (2018).

Article  CAS  PubMed  Google Scholar 

Miller, M. B. et al. Somatic genomic changes in single Alzheimer’s disease neurons. Nature 604, 714–722 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bizzotto, S. & Walsh, C. A. Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders. Nat. Rev. Neurosci. 23, 275–286 (2022).

Article  CAS  PubMed  Google Scholar 

Proukakis, C. Somatic mutations in neurodegeneration: an update. Neurobiol. Dis. 144, 105021 (2020).

Article  CAS  PubMed  Google Scholar 

Voet, T. & Vermeesch, J. R. Mutational processes shaping the genome in early human embryos. Cell 168, 751–753 (2017).

Article  CAS  PubMed  Google Scholar 

van Neerven, S. M. & Vermeulen, L. Cell competition in development, homeostasis and cancer. Nat. Rev. Mol. Cell Biol. https://doi.org/10.1038/s41580-022-00538-y (2022).

Article  PubMed  Google Scholar 

Ren, P., Dong, X. & Vijg, J. Age-related somatic mutation burden in human tissues. Front. Aging 3, 1018119 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Bekaert, B. et al. CRISPR/Cas gene editing in the human germline. Semin. Cell Dev. Biol. 131, 93–107 (2022).

Article  CAS  PubMed  Google Scholar 

Alanis-Lobato, G. et al. Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos. Proc. Natl Acad. Sci. USA 118, e2004832117 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fogarty, N. M. E. et al. Genome editing reveals a role for OCT4 in human embryogenesis. Nature 550, 67–73 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sheth, R. U. & Wang, H. H. DNA-based memory devices for recording cellular events. Nat. Rev. Genet. 19, 718–732 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bhattarai-Kline, S. et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature 608, 217–225 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choi, J. et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature 608, 98–107 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, L. et al. Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat. Commun. 10, 470 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cheng, H. et al.Smart3-ATAC: a highly sensitive method for joint accessibility and full-length transcriptome analysis in singlecells. Preprint at bioRxiv https://doi.org/10.1101/2021.12.02.470912 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380–1385 (2018).

Article