과제정보
This work was supported by the National Research Foundation (NRF) of Korea (2021R1F1A104962311) and the Gachon University Research Fund (GCU-202102820001).
참고문헌
- Abdelmoez, M.N., Iida, K., Oguchi, Y., Nishikii, H., Yokokawa, R., Kotera, H., Uemura, S., Santiago, J.G., and Shintaku, H. (2018). SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology. Genome Biol. 19, 66.
- Angerer, P., Simon, L., Tritschler, S., Wolf, F.A., Fischer, D., and Theis, F.J. (2017). Single cells make big data: new challenges and opportunities in transcriptomics. Curr. Opin. Syst. Biol. 4, 85-91. https://doi.org/10.1016/j.coisb.2017.07.004
- Bian, S., Hou, Y., Zhou, X., Li, X., Yong, J., Wang, Y., Wang, W., Yan, J., Hu, B., Guo, H., et al. (2018). Single-cell multiomics sequencing and analyses of human colorectal cancer. Science 362, 1060-1063. https://doi.org/10.1126/science.aao3791
- Bhang, H.E.C., Ruddy, D.A., Krishnamurthy Radhakrishna, V., Caushi, J.X., Zhao, R., Hims, M.M., Singh, A.P., Kao, I., Rakiec, D., Shaw, P., et al. (2015). Studying clonal dynamics in response to cancer therapy using high-complexity barcoding. Nat. Med. 21, 440-448. https://doi.org/10.1038/nm.3841
- Buenrostro, J.D., Corces, M.R., Lareau, C.A., Wu, B., Schep, A.N., Aryee, M.J., Majeti, R., Chang, H.Y., and Greenleaf, W.J. (2018). Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation. Cell 173, 1535-1548.e16. https://doi.org/10.1016/j.cell.2018.03.074
- Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., and Greenleaf, W.J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218. https://doi.org/10.1038/nmeth.2688
- Cao, J., Cusanovich, D.A., Ramani, V., Aghamirzaie, D., Pliner, H.A., Hill, A.J., Daza, R.M., McFaline-Figueroa, J.L., Packer, J.S., Christiansen, L., et al. (2018). Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380-1385. https://doi.org/10.1126/science.aau0730
- Cao, J., Packer, J.S., Ramani, V., Cusanovich, D.A., Huynh, C., Daza, R., Qiu, X., Lee, C., Furlan, S.N., Steemers, F.J., et al. (2017). Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661-667. https://doi.org/10.1126/science.aam8940
- Chan, M.M., Smith, Z.D., Grosswendt, S., Kretzmer, H., Norman, T.M., Adamson, B., Jost, M., Quinn, J.J., Yang, D., Jones, M.G., et al. (2019). Molecular recording of mammalian embryogenesis. Nature 570, 77-82. https://doi.org/10.1038/s41586-019-1184-5
- Chappell, L., Russell, A.J.C., and Voet, T. (2018). Single-cell (multi)omics technologies. Annu. Rev. Genomics Hum. Genet. 19, 15-41. https://doi.org/10.1146/annurev-genom-091416-035324
- Chen, A.F., Parks, B., Kathiria, A.S., Ober-Reynolds, B., Goronzy, J.J., and Greenleaf, W.J. (2022). NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. Nat. Methods 19, 547-553. https://doi.org/10.1038/s41592-022-01461-y
- Chen, S., Lake, B.B., and Zhang, K. (2019). High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat. Biotechnol. 37, 1452-1457. https://doi.org/10.1038/s41587-019-0290-0
- Choi, J., Chen, W., Minkina, A., Chardon, F.M., Suiter, C.C., Regalado, S.G., Domcke, S., Hamazaki, N., Lee, C., Martin, B., et al. (2022). A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature 608, 98-107. https://doi.org/10.1038/s41586-022-04922-8
- Choi, Y.H. and Kim, J.K. (2019). Dissecting cellular heterogeneity using single-cell RNA sequencing. Mol. Cells 42, 189-199.
- Chung, H., Parkhurst, C.N., Magee, E.M., Phillips, D., Habibi, E., Chen, F., Yeung, B.Z., Waldman, J., Artis, D., and Regev, A. (2021). Joint single-cell measurements of nuclear proteins and RNA in vivo. Nat. Methods 18, 1204-1212. https://doi.org/10.1038/s41592-021-01278-1
- Clark, S.J., Argelaguet, R., Kapourani, C.A., Stubbs, T.M., Lee, H.J., AldaCatalinas, C., Krueger, F., Sanguinetti, G., Kelsey, G., Marioni, J.C., et al. (2018). scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat. Commun. 9, 781.
- Datlinger, P., Rendeiro, A.F., Boenke, T., Senekowitsch, M., Krausgruber, T., Barreca, D., and Bock, C. (2021). Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing. Nat. Methods 18, 635-642. https://doi.org/10.1038/s41592-021-01153-z
- Dey, S.S., Kester, L., Spanjaard, B., Bienko, M., and van Oudenaarden, A. (2015). Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 33, 285-289. https://doi.org/10.1038/nbt.3129
- Di, L., Fu, Y., Sun, Y., Li, J., Liu, L., Yao, J., Wang, G., Wu, Y., Lao, K., Lee, R.W., et al. (2020). RNA sequencing by direct tagmentation of RNA/DNA hybrids. Proc. Natl. Acad. Sci. U. S. A. 117, 2886-2893. https://doi.org/10.1073/pnas.1919800117
- Dimitriu, M.A., Lazar-Contes, I., Roszkowski, M., and Mansuy, I.M. (2022). Single-cell multiomics techniques: from conception to applications. Front. Cell Dev. Biol. 10, 854317.
- Dominguez Conde, C., Xu, C., Jarvis, L.B., Rainbow, D.B., Wells, S.B., Gomes, T., Howlett, S.K., Suchanek, O., Polanski, K., King, H.W., et al. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 376, eabl5197.
- Elmentaite, R., Dominguez Conde, C., Yang, L., and Teichmann, S.A. (2022). Single-cell atlases: shared and tissue-specific cell types across human organs. Nat. Rev. Genet. 23, 395-410. https://doi.org/10.1038/s41576-022-00449-w
- Eng, C.H.L., Lawson, M., Zhu, Q., Dries, R., Koulena, N., Takei, Y., Yun, J., Cronin, C., Karp, C., Yuan, G.C., et al. (2019). Transcriptome-scale superresolved imaging in tissues by RNA seqFISH. Nature 568, 235-239. https://doi.org/10.1038/s41586-019-1049-y
- Eraslan, G., Drokhlyansky, E., Anand, S., Fiskin, E., Subramanian, A., Slyper, M., Wang, J., Van Wittenberghe, N., Rouhana, J.M., Waldman, J., et al. (2022). Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function. Science 376, eabl4290.
- Eyler, C.E., Matsunaga, H., Hovestadt, V., Vantine, S.J., van Galen, P., and Bernstein, B.E. (2020). Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol. 21, 174.
- Eze, U.C., Bhaduri, A., Haeussler, M., Nowakowski, T.J., and Kriegstein, A.R. (2021). Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat. Neurosci. 24, 584-594. https://doi.org/10.1038/s41593-020-00794-1
- Fang, L., Li, G., Sun, Z., Zhu, Q., Cui, H., Li, Y., Zhang, J., Liang, W., Wei, W., Hu, Y., et al. (2021). CASB: a concanavalin A-based sample barcoding strategy for single-cell sequencing. Mol. Syst. Biol. 17, e10060.
- Fiskin, E., Lareau, C.A., Ludwig, L.S., Eraslan, G., Liu, F., Ring, A.M., Xavier, R.J., and Regev, A. (2022). Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nat. Biotechnol. 40, 374-381. https://doi.org/10.1038/s41587-021-01065-5
- Frei, A.P., Bava, F.A., Zunder, E.R., Hsieh, E.W.Y., Chen, S.Y., Nolan, G.P., and Gherardini, P.F. (2016). Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat. Methods 13, 269-275. https://doi.org/10.1038/nmeth.3742
- Frieda, K.L., Linton, J.M., Hormoz, S., Choi, J., Chow, K.H.K., Singer, Z.S., Budde, M.W., Elowitz, M.B., and Cai, L. (2017). Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107-111. https://doi.org/10.1038/nature20777
- Genshaft, A.S., Li, S., Gallant, C.J., Darmanis, S., Prakadan, S.M., Ziegler, C.G.K., Lundberg, M., Fredriksson, S., Hong, J., Regev, A., et al. (2016). Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. Genome Biol. 17, 188.
- Gerlach, J.P., van Buggenum, J.A.G., Tanis, S.E.J., Hogeweg, M., Heuts, B.M.H., Muraro, M.J., Elze, L., Rivello, F., Rakszewska, A., van Oudenaarden, A., et al. (2019). Combined quantification of intracellular (phospho-) proteins and transcriptomics from fixed single cells. Sci. Rep. 9, 1469.
- Gu, C., Liu, S., Wu, Q., Zhang, L., and Guo, F. (2019). Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes. Cell Res. 29, 110-123. https://doi.org/10.1038/s41422-018-0125-4
- Han, K.Y., Kim, K.T., Joung, J.G., Son, D.S., Kim, Y.J., Jo, A., Jeon, H.J., Moon, H.S., Yoo, C.E., Chung, W., et al. (2018). SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells. Genome Res. 28, 75-87. https://doi.org/10.1101/gr.223263.117
- He, S., Wang, L.H., Liu, Y., Li, Y.Q., Chen, H.T., Xu, J.H., Peng, W., Lin, G.W., Wei, P.P., Li, B., et al. (2020). Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs. Genome Biol. 21, 294.
- Hu, Y., Huang, K., An, Q., Du, G., Hu, G., Xue, J., Zhu, X., Wang, C.Y., Xue, Z., and Fan, G. (2016). Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 17, 88.
- Hu, Y., Zhong, J., Xiao, Y., Xing, Z., Sheu, K., Fan, S., An, Q., Qiu, Y., Zheng, Y., Liu, X., et al. (2020). Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation. Nat. Commun. 11, 5148.
- Janssens, D.H., Otto, D.J., Meers, M.P., Setty, M., Ahmad, K., and Henikoff, S. (2022). CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells. Genome Biol. 23, 81.
- Jiang, Y.R., Zhu, L., Cao, L.R., Wu, Q., Chen, J.B., Wang, Y., Wu, J., Zhang, T.Y., Wang, Z.L., Guan, Z.Y., et al. (2022). Simultaneous transcriptome and proteome profiling in a single mouse oocyte with a deep single-cell multiomics approach. BioRxiv, https://doi.org/10.1101/2022.08.17.504335
- Jovic, D., Liang, X., Zeng, H., Lin, L., Xu, F., and Luo, Y. (2022). Single-cell RNA sequencing technologies and applications: a brief overview. Clin. Transl. Med. 12, e694.
- Kim, I.S., Wu, J., Rahme, G.J., Battaglia, S., Dixit, A., Gaskell, E., Chen, H., Pinello, L., and Bernstein, B.E. (2020). Parallel single-cell RNA-seq and genetic recording reveals lineage decisions in developing embryoid bodies. Cell Rep. 33, 108222.
- Kumar, V., Ramnarayanan, K., Sundar, R., Padmanabhan, N., Srivastava, S., Koiwa, M., Yasuda, T., Koh, V., Huang, K.K., Tay, S.T., et al. (2022). Singlecell atlas of lineage states, tumor microenvironment, and subtype-specific expression programs in gastric cancer. Cancer Discov. 12, 670-691. https://doi.org/10.1158/2159-8290.CD-21-0683
- Lee, D.S., Luo, C., Zhou, J., Chandran, S., Rivkin, A., Bartlett, A., Nery, J.R., Fitzpatrick, C., O'Connor, C., Dixon, J.R., et al. (2019). Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat. Methods 16, 999-1006. https://doi.org/10.1038/s41592-019-0547-z
- Lee, J., Hyeon, D.Y., and Hwang, D. (2020). Single-cell multiomics: technologies and data analysis methods. Exp. Mol. Med. 52, 1428-1442. https://doi.org/10.1038/s12276-020-0420-2
- Lee, S., Kim, J., and Park, J.E. (2021). Single-cell toolkits opening a new era for cell engineering. Mol. Cells 44, 127-135. https://doi.org/10.14348/molcells.2021.0002
- Li, G., Liu, Y., Zhang, Y., Kubo, N., Yu, M., Fang, R., Kellis, M., and Ren, B. (2019). Joint profiling of DNA methylation and chromatin architecture in single cells. Nat. Methods 16, 991-993. https://doi.org/10.1038/s41592-019-0502-z
- Liu, L., Liu, C., Quintero, A., Wu, L., Yuan, Y., Wang, M., Cheng, M., Leng, L., Xu, L., Dong, G., et al. (2019). Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat. Commun. 10, 470.
- Loveless, T.B., Grotts, J.H., Schechter, M.W., Forouzmand, E., Carlson, C.K., Agahi, B.S., Liang, G., Ficht, M., Liu, B., Xie, X., et al. (2021). Lineage tracing and analog recording in mammalian cells by single-site DNA writing. Nat. Chem. Biol. 17, 739-747. https://doi.org/10.1038/s41589-021-00769-8
- Lu, B., Dong, L., Yi, D., Zhang, M., Zhu, C., Li, X., and Yi, C. (2020). Transposase-assisted tagmentation of RNA/DNA hybrid duplexes. Elife 9, e54919.
- Lu, Y., Yang, A., Quan, C., Pan, Y., Zhang, H., Li, Y., Gao, C., Lu, H., Wang, X., Cao, P., et al. (2022). A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma. Nat. Commun. 13, 4594.
- Luo, C., Liu, H., Xie, F., Armand, E.J., Siletti, K., Bakken, T.E., Fang, R., Doyle, W.I., Stuart, T., Hodge, R.D., et al. (2022). Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2, 100106.
- Ma, S., Zhang, B., LaFave, L.M., Earl, A.S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V.K., Tay, T., et al. (2020). Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183, 1103-1116.e20. https://doi.org/10.1016/j.cell.2020.09.056
- Macaulay, I.C., Haerty, W., Kumar, P., Li, Y.I., Hu, T.X., Teng, M.J., Goolam, M., Saurat, N., Coupland, P., Shirley, L.M., et al. (2015). G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519-522. https://doi.org/10.1038/nmeth.3370
- Macosko, E.Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A.R., Kamitaki, N., Martersteck, E.M., et al. (2015). Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202-1214. https://doi.org/10.1016/j.cell.2015.05.002
- McGinnis, C.S., Patterson, D.M., Winkler, J., Conrad, D.N., Hein, M.Y., Srivastava, V., Hu, J.L., Murrow, L.M., Weissman, J.S., Werb, Z., et al. (2019). MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat. Methods 16, 619-626. https://doi.org/10.1038/s41592-019-0433-8
- Mimitou, E.P., Cheng, A., Montalbano, A., Hao, S., Stoeckius, M., Legut, M., Roush, T., Herrera, A., Papalexi, E., Ouyang, Z., et al. (2019). Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. Nat. Methods 16, 409-412. https://doi.org/10.1038/s41592-019-0392-0
- Mimitou, E.P., Lareau, C.A., Chen, K.Y., Zorzetto-Fernandes, A.L., Hao, Y., Takeshima, Y., Luo, W., Huang, T.S., Yeung, B.Z., Papalexi, E., et al. (2021). Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol. 39, 1246-1258. https://doi.org/10.1038/s41587-021-00927-2
- Nomura, S. (2021). Single-cell genomics to understand disease pathogenesis. J. Hum. Genet. 66, 75-84. https://doi.org/10.1038/s10038-020-00844-3
- Park, S., Mali, N.M., Kim, R., Choi, J.W., Lee, J., Lim, J., Park, J.M., Park, J.W., Kim, D., Kim, T., et al. (2021). Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 597, 393-397. https://doi.org/10.1038/s41586-021-03786-8
- Perkel, J.M. (2021). Single-cell analysis enters the multiomics age. Nature 595, 614-616. https://doi.org/10.1038/d41586-021-01994-w
- Peterson, V.M., Zhang, K.X., Kumar, N., Wong, J., Li, L., Wilson, D.C., Moore, R., McClanahan, T.K., Sadekova, S., and Klappenbach, J.A. (2017). Multiplexed quantification of proteins and transcripts in single cells. Nat. Biotechnol. 35, 936-939. https://doi.org/10.1038/nbt.3973
- Picelli, S., Faridani, O.R., Bjorklund, A.K., Winberg, G., Sagasser, S., and Sandberg, R. (2014). Full-length RNA-seq from single cells using Smartseq2. Nat. Protoc. 9, 171-181. https://doi.org/10.1038/nprot.2014.006
- Prakadan, S.M., Shalek, A.K., and Weitz, D.A. (2017). Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. Nat. Rev. Genet. 18, 345-361. https://doi.org/10.1038/nrg.2017.15
- Raj, B., Gagnon, J.A., and Schier, A.F. (2018). Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR-Cas9 barcodes by scGESTALT. Nat. Protoc. 13, 2685-2713. https://doi.org/10.1038/s41596-018-0058-x
- Reyes, M., Billman, K., Hacohen, N., and Blainey, P.C. (2019). Simultaneous profiling of gene expression and chromatin accessibility in single cells. Adv. Biosyst. 3, 1900065.
- Rodriguez-Meira, A., Buck, G., Clark, S.A., Povinelli, B.J., Alcolea, V., Louka, E., McGowan, S., Hamblin, A., Sousos, N., Barkas, N., et al. (2019). Unravelling intratumoral heterogeneity through high-sensitivity single-cell mutational analysis and parallel RNA sequencing. Mol. Cell 73, 1292-1305.e8. https://doi.org/10.1016/j.molcel.2019.01.009
- Rodriques, S.G., Stickels, R.R., Goeva, A., Martin, C.A., Murray, E., Vanderburg, C.R., Welch, J., Chen, L.M., Chen, F., and Macosko, E.Z. (2019). Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463-1467. https://doi.org/10.1126/science.aaw1219
- Rooijers, K., Markodimitraki, C.M., Rang, F.J., de Vries, S.S., Chialastri, A., de Luca, K.L., Mooijman, D., Dey, S.S., and Kind, J. (2019). Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells. Nat. Biotechnol. 37, 766-772. https://doi.org/10.1038/s41587-019-0150-y
- Rosenberg, A.B., Roco, C.M., Muscat, R.A., Kuchina, A., Sample, P., Yao, Z., Graybuck, L.T., Peeler, D.J., Mukherjee, S., Chen, W., et al. (2018). Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176-182. https://doi.org/10.1126/science.aam8999
- Rubin, A.J., Parker, K.R., Satpathy, A.T., Qi, Y., Wu, B., Ong, A.J., Mumbach, M.R., Ji, A.L., Kim, D.S., Cho, S.W., et al. (2019). Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks. Cell 176, 361-376.e17. https://doi.org/10.1016/j.cell.2018.11.022
- Shalek, A.K., Satija, R., Adiconis, X., Gertner, R.S., Gaublomme, J.T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013). Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236-240. https://doi.org/10.1038/nature12172
- Stoeckius, M., Hafemeister, C., Stephenson, W., Houck-Loomis, B., Chattopadhyay, P.K., Swerdlow, H., Satija, R., and Smibert, P. (2017). Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865-868. https://doi.org/10.1038/nmeth.4380
- Strzelecka, P.M., Ranzoni, A.M., and Cvejic, A. (2018). Dissecting human disease with single-cell omics: application in model systems and in the clinic. Dis. Model. Mech. 11, dmm036525.
- Suo, C., Dann, E., Goh, I., Jardine, L., Kleshchevnikov, V., Park, J.E., Botting, R.A., Stephenson, E., Engelbert, J., Tuong, Z.K., et al. (2022). Mapping the developing human immune system across organs. Science 376, eabo0510.
- Swanson, E., Lord, C., Reading, J., Heubeck, A.T., Genge, P.C., Thomson, Z., Weiss, M.D.A., Li, X.J., Savage, A.K., Green, R.R., et al. (2021). Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq. Elife 10, e63632.
- Tabula Sapiens Consortium, Jones, R.C., Karkanias, J., Krasnow, M.A., Pisco, A.O., Quake, S.R., Salzman, J., Yosef, N., Bulthaup, B., Brown, P., et al. (2022). The Tabula Sapiens: a multiple-organ, single-cell transcriptomic atlas of humans. Science 376, eabl4896.
- Tang, X., Huang, Y., Lei, J., Luo, H., and Zhu, X. (2019). The single-cell sequencing: new developments and medical applications. Cell Biosci. 9, 53.
- Unterman, A., Sumida, T.S., Nouri, N., Yan, X., Zhao, A.Y., Gasque, V., Schupp, J.C., Asashima, H., Liu, Y., Cosme, C., Jr., et al. (2022). Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat. Commun. 13, 440.
- Wang, D. and Bodovitz, S. (2010). Single cell analysis: the new frontier in 'omics'. Trends Biotechnol. 28, 281-290. Wang, Y., Yuan, P., Yan, Z., Yang, M., Huo, Y., Nie, Y., Zhu, X., Qiao, J., and https://doi.org/10.1016/j.tibtech.2010.03.002
- Yan, L. (2021). Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos. Nat. Commun. 12, 1247.
- Wei, C.J.Y. and Zhang, K. (2020). RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. Genome Res. 30, 602-610. https://doi.org/10.1101/gr.255851.119
- Weinreb, C., Rodriguez-Fraticelli, A., Camargo, F.D., and Klein, A.M. (2020). Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science 367, eaaw3381.
- Weinreb, C., Wolock, S., Tusi, B.K., Socolovsky, M., and Klein, A.M. (2018). Fundamental limits on dynamic inference from single-cell snapshots. Proc. Natl. Acad. Sci. U. S. A. 115, E2467-E2476. https://doi.org/10.1073/pnas.1714723115
- Williams, C.G., Lee, H.J., Asatsuma, T., Vento-Tormo, R., and Haque, A. (2022). An introduction to spatial transcriptomics for biomedical research. Genome Med. 14, 68.
- Xing, Q.R., Farran, C.A.E., Zeng, Y.Y., Yi, Y., Warrier, T., Gautam, P., Collins, J.J., Xu, J., Droge, P., Koh, C.G., et al. (2020). Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility. Genome Res. 30, 1027-1039. https://doi.org/10.1101/gr.257840.119
- Xu, W., Yang, W., Zhang, Y., Chen, Y., Hong, N., Zhang, Q., Wang, X., Hu, Y., Song, K., Jin, W., et al. (2022). ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells. Nat. Methods 19, 1243-1249. https://doi.org/10.1038/s41592-022-01601-4
- Yan, R., Gu, C., You, D., Huang, Z., Qian, J., Yang, Q., Cheng, X., Zhang, L., Wang, H., Wang, P., et al. (2021). Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing. Cell Stem Cell 28, 1641-1656.e7. https://doi.org/10.1016/j.stem.2021.04.012
- Zhang, L., Yu, X., Zheng, L., Zhang, Y., Li, Y., Fang, Q., Gao, R., Kang, B., Zhang, Q., Huang, J.Y., et al. (2018). Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature 564, 268-272. https://doi.org/10.1038/s41586-018-0694-x
- Zhu, C., Yu, M., Huang, H., Juric, I., Abnousi, A., Hu, R., Lucero, J., Behrens, M.M., Hu, M., and Ren, B. (2019). An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat. Struct. Mol. Biol. 26, 1063-1070. https://doi.org/10.1038/s41594-019-0323-x