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Single-cell sequencing has become one of the most powerful and popular techniques in dissecting molecular heterogeneity and modeling the cellular architecture of a biological system. During the past twenty years, the throughput of single-cell sequencing has increased from hundreds of cells to over tens of thousands of cells in parallel. Moreover, this technology has been developed from sequencing transcriptome to measure different omics such as DNA methylome, chromatin accessibility, and so on. Currently, multi-omics which can analyze different omics in the same cell is rapidly advancing. This work advances the study of many biosystems, including the nervous system. Here, we review current single-cell multi-omics sequencing techniques and describe how they improve our understanding of the nervous system. Finally, we discuss the open scientific questions in neural research that may be answered through further improvement of single-cell multi-omics sequencing technology.

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Single-cell multi-omics sequencing and its applications in studying the nervous system

Show Author's information Chaoyang Wang1Xiaoying Fan1,2( )
Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510700, China


Single-cell sequencing has become one of the most powerful and popular techniques in dissecting molecular heterogeneity and modeling the cellular architecture of a biological system. During the past twenty years, the throughput of single-cell sequencing has increased from hundreds of cells to over tens of thousands of cells in parallel. Moreover, this technology has been developed from sequencing transcriptome to measure different omics such as DNA methylome, chromatin accessibility, and so on. Currently, multi-omics which can analyze different omics in the same cell is rapidly advancing. This work advances the study of many biosystems, including the nervous system. Here, we review current single-cell multi-omics sequencing techniques and describe how they improve our understanding of the nervous system. Finally, we discuss the open scientific questions in neural research that may be answered through further improvement of single-cell multi-omics sequencing technology.

Keywords: Nervous system, Multi-omics, Single-cell sequencing, Cell heterogeneity


Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W (2016) Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods 13(3): 229−232

Armand EJ, Li J, Xie F, Luo C, Mukamel EA (2021) Single-cell sequencing of brain cell transcriptomes and epigenomes. Neuron 109(1): 11−26

Aslam B, Basit M, Nisar MA, Khurshid M, Rasool MH (2017) Proteomics: technologies and their applications. J Chromatogr Sci 55(2): 182−196

Bailey K, Rahimi Balaei M, Mannan A, Del Bigio MR, Marzban H (2014) Purkinje cell compartmentation in the cerebellum of the lysosomal acid phosphatase 2 mutant mouse (nax - naked-ataxia mutant mouse). PLoS One 9(4): e94327.

Banaszynski LA, Wen DC, Dewell S, Whitcomb SJ, Lin MY, Diaz N, Elsasser SJ, Chapgier A, Goldberg AD, Canaani E, Rafii S, Zheng DY, Allis CD (2013) Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 155(1): 107−120

Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3): 381−395

Barmack NH, Qian Z, Yoshimura J (2000) Regional and cellular distribution of protein kinase C in rat cerebellar Purkinje cells. J Comp Neurol 427(2): 235−254

Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4): 823−837

Basak O, Giachino C, Fiorini E, Macdonald HR, Taylor V (2012) Neurogenic subventricular zone stem/progenitor cells are Notch1-dependent in their active but not quiescent state. J Neurosci 32(16): 5654−5666

Bengoa-Vergniory N, Kypta RM (2015) Canonical and noncanonical Wnt signaling in neural stem/progenitor cells. Cell Mol Life Sci 72(21): 4157−4172

Bian S, Hou Y, Zhou X, Li X, Yong J, Wang Y, Wang W, Yan J, Hu B, Guo H, Wang J, Gao S, Mao Y, Dong J, Zhu P, Xiu D, Yan L, Wen L, Qiao J, Tang F, Fu W (2018) Single-cell multiomics sequencing and analyses of human colorectal cancer. Science 362(6418): 1060−1063

Breijyeh Z, Karaman R (2020) Comprehensive review on Alzheimer’s disease: causes and treatment. Molecules 25: 24.

Brochu G, Maler L, Hawkes R (1990) Zebrin II: a polypeptide antigen expressed selectively by Purkinje cells reveals compartments in rat and fish cerebellum. J Comp Neurol 291(4): 538−552

Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J (2018) Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361(6409): 1380−1385

Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J (2019) The single-cell transcriptional landscape of mammalian organogenesis. Nature 566(7745): 496−502

Cardona-Alberich A, Tourbez M, Pearce SF, Sibley CR (2021) Elucidating the cellular dynamics of the brain with single-cell RNA sequencing. RNA Biol.

Chen CYA, Ezzeddine N, Shyu AB (2008) Chapter 17 Messenger RNA half‐life measurements in mammalian cells. In: RNA turnover in eukaryotes: nucleases, pathways and analysis of mRNA decay. pp 335-357.

Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X (2015) RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348(6233): aaa6090.

Chen S, Lake BB, Zhang K (2019) High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat Biotechnol 37(12): 1452−1457

Cheow LF, Courtois ET, Tan Y, Viswanathan R, Xing Q, Tan RZ, Tan DS, Robson P, Loh YH, Quake SR, Burkholder WF (2016) Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. Nat Methods 13(10): 833−836

Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W (2018) scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells. Nat Commun 9(1): 781.

Clayton AL, Hebbes TR, Thorne AW, Crane-Robinson C (1993) Histone acetylation and gene induction in human cells. FEBS Lett 336(1): 23−26

Colomé-Tatché M, Theis FJ (2018) Statistical single cell multi-omics integration. Curr Opin Syst Biol 7: 54−59

Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, Boyer LA, Young RA, Jaenisch R (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107(50): 21931−21936

Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J (2018) A single-cell atlas of in vivo mammalian chromatin accessibility. Cell 174(5): 1309−1324

Demilly A, Reeber SL, Gebre SA, Sillitoe RV (2011) Neurofilament heavy chain expression reveals a unique parasagittal stripe topography in the mouse cerebellum. Cerebellum 10(3): 409−421

Dulken BW, Buckley MT, Navarro Negredo P, Saligrama N, Cayrol R, Leeman DS, George BM, Boutet SC, Hebestreit K, Pluvinage JV, Wyss-Coray T, Weissman IL, Vogel H, Davis MM, Brunet A (2019) Single-cell analysis reveals T cell infiltration in old neurogenic niches. Nature 571(7764): 205−210

Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L (2019) Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. Nature 568(7751): 235−239

Engler A, Zhang R, Taylor V (2018) Notch and neurogenesis. Adv Exp Med Biol 1066: 223−234

Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF (2016) Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods 13(3): 269−275

Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, Lundberg M, Fredriksson S, Hong J, Regev A, Livak KJ, Landegren U, Shalek AK (2016) Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. Genome Biol 17(1): 188.

Gravel C, Hawkes R (1990) Parasagittal organization of the rat cerebellar cortex: direct comparison of Purkinje cell compartments and the organization of the spinocerebellar projection. J Comp Neurol 291(1): 79−102

Grosselin K, Durand A, Marsolier J, Poitou A, Marangoni E, Nemati F, Dahmani A, Lameiras S, Reyal F, Frenoy O, Pousse Y, Reichen M, Woolfe A, Brenan C, Griffiths AD, Vallot C, Gerard A (2019) High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer. Nat Genet 51(6): 1060−1066

Grove J, Ripke S, Als TD, Mattheisen M, Walters RK, Won H, Pallesen J, Agerbo E, Andreassen OA, Anney R, Awashti S, Belliveau R, Bettella F, Buxbaum JD, Bybjerg-Grauholm J, Baekvad-Hansen M, Cerrato F, Chambert K, Christensen JH, Churchhouse C, Dellenvall K, Demontis D, De Rubeis S, Devlin B, Djurovic S, Dumont AL, Goldstein JI, Hansen CS, Hauberg ME, Hollegaard MV, Hope S, Howrigan DP, Huang H, Hultman CM, Klei L, Maller J, Martin J, Martin AR, Moran JL, Nyegaard M, Naerland T, Palmer DS, Palotie A, Pedersen CB, Pedersen MG, dPoterba T, Poulsen JB, Pourcain BS, Qvist P, Rehnstrom K, Reichenberg A, Reichert J, Robinson EB, Roeder K, Roussos P, Saemundsen E, Sandin S, Satterstrom FK, Davey Smith G, Stefansson H, Steinberg S, Stevens CR, Sullivan PF, Turley P, Walters GB, Xu X, Autism Spectrum Disorder Working Group of the Psychiatric Genomics C, Bupgen, Major Depressive Disorder Working Group of the Psychiatric Genomics C, 23andMe Research T, Stefansson K, Geschwind DH, Nordentoft M, Hougaard DM, Werge T, Mors O, Mortensen PB, Neale BM, Daly MJ, Borglum AD (2019) Identification of common genetic risk variants for autism spectrum disorder. Nat Genet 51(3): 431−444

Gu C, Liu S, Wu Q, Zhang L, Guo F (2019) Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes. Cell Res 29(2): 110−123

Guo F, Li L, Li J, Wu X, Hu B, Zhu P, Wen L, Tang F (2017a) Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells. Cell Res 27(8): 967−988

Guo H, Hu B, Yan L, Yong J, Wu Y, Gao Y, Guo F, Hou Y, Fan X, Dong J, Wang X, Zhu X, Yan J, Wei Y, Jin H, Zhang W, Wen L, Tang F, Qiao J (2017b) DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells. Cell Res 27(2): 165−183

Hatakeyama J, Bessho Y, Katoh K, Ookawara S, Fujioka M, Guillemot F, Kageyama R (2004) Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation. Development 131(22): 5539−5550

Hohn T, Corsten S, Rieke S, Muller M, Rothnie H (1996) Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci USA 93(16): 8334−8339

Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B (2013) Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet 45(10): 1198−1206

Hou Y, Guo H, Cao C, Li X, Hu B, Zhu P, Wu X, Wen L, Tang F, Huang Y, Peng J (2016) Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res 26(3): 304−319

Hrvatin S, Hochbaum DR, Nagy MA, Cicconet M, Robertson K, Cheadle L, Zilionis R, Ratner A, Borges-Monroy R, Klein AM, Sabatini BL, Greenberg ME (2018) Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat Neurosci 21(1): 120−129

Hu P, Fabyanic E, Kwon DY, Tang S, Zhou Z, Wu H (2017) Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-Seq. Mol Cell 68(5): 1006−1015

Hu Y, Huang K, An Q, Du G, Hu G, Xue J, Zhu X, Wang CY, Xue Z, Fan G (2016) Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol 17: 88.

Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M (2014) The contribution of de novo coding mutations to autism spectrum disorder. Nature 515(7526): 216−221

Jones PA (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13(7): 484−492

Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S (2019) CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun 10(1): 1930.

Kozlenkov A, Wang M, Roussos P, Rudchenko S, Barbu M, Bibikova M, Klotzle B, Dwork AJ, Zhang B, Hurd YL, Koonin EV, Wegner M, Dracheva S (2016) Substantial DNA methylation differences between two major neuronal subtypes in human brain. Nucleic Acids Res 44(6): 2593−2612

Krol AJ, Roellig D, Dequeant ML, Tassy O, Glynn E, Hattem G, Mushegian A, Oates AC, Pourquie O (2011) Evolutionary plasticity of segmentation clock networks. Development 138(13): 2783−2792

Labib M, Kelley SO (2020) Single-cell analysis targeting the proteome. Nat Rev Chem 4(3): 143−158

Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K (2018) Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat Biotechnol 36(1): 70−80

Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR (2019) Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat Methods 16(10): 999−1006

Lein E, Borm LE, Linnarsson S (2017) The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing. Science 358(6359): 64−69

Li F, Wan M, Zhang B, Peng Y, Zhou Y, Pi C, Xu X, Ye L, Zhou X, Zheng L (2018) Bivalent histone modifications and development. Curr Stem Cell Res Ther 13(2): 83−90

Li G, Liu Y, Zhang Y, Kubo N, Yu M, Fang R, Kellis M, Ren B (2019) Joint profiling of DNA methylation and chromatin architecture in single cells. Nat Methods 16(10): 991−993

Liao J, Lu X, Shao X, Zhu L, Fan X (2021) Uncovering an organ's molecular architecture at single-cell resolution by spatially resolved transcriptomics. Trends Biotechnol 39(1): 43−58

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950): 289−293

Liu L, Liu C, Quintero A, Wu L, Yuan Y, Wang M, Cheng M, Leng L, Xu L, Dong G, Li R, Liu Y, Wei X, Xu J, Chen X, Lu H, Chen D, Wang Q, Zhou Q, Lin X, Li G, Liu S, Wang Q, Wang H, Fink JL, Gao Z, Liu X, Hou Y, Zhu S, Yang H, Ye Y, Lin G, Chen F, Herrmann C, Eils R, Shang Z, Xu X (2019) Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat Commun 10(1): 470.

Llorens-Bobadilla E, Chell JM, Le Merre P, Wu Y, Zamboni M, Bergenstrahle J, Stenudd M, Sopova E, Lundeberg J, Shupliakov O, Carlen M, Frisen J (2020) A latent lineage potential in resident neural stem cells enables spinal cord repair. Science 370: 6512.

Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, Ecker JR (2017) Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science 357(6351): 600−604

Luo C, Liu H, Wang B-A, Bartlett A, Rivkin A, Nery JR, Ecker JR (2018) Multi-omic profiling of transcriptome and DNA methylome in single nuclei with molecular partitioning. bioRxiv.

Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Hodge RD, Hu L, Wang B-A, Zhang Z, Preissl S, Lee D-S, Zhou J, Niu S-Y, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR (2019) Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants. bioRxiv.

Ma A, McDermaid A, Xu J, Chang Y, Ma Q (2020a) Integrative methods and practical challenges for single-cell multi-omics. Trends Biotechnol 38(9): 1007−1022

Ma S, Zhang B, LaFave LM, Earl AS, Chiang Z, Hu Y, Ding J, Brack A, Kartha VK, Tay T, Law T, Lareau C, Hsu YC, Regev A, Buenrostro JD (2020b) Chromatin potential identified by shared single-cell profiling of RNA and chromatin. Cell 183(4): 1103−1116

Maniatis S, Aijo T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivova Z, Saarenpaa S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H (2019) Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science 364(6435): 89−93

Maze I, Wenderski W, Noh KM, Bagot RC, Tzavaras N, Purushothaman I, Elsasser SJ, Guo Y, Ionete C, Hurd YL, Tamminga CA, Halene T, Farrelly L, Soshnev AA, Wen D, Rafii S, Birtwistle MR, Akbarian S, Buchholz BA, Blitzer RD, Nestler EJ, Yuan ZF, Garcia BA, Shen L, Molina H, Allis CD (2015) Critical role of histone turnover in neuronal transcription and plasticity. Neuron 87(1): 77−94

Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J (2015) Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86(6): 1369−1384

Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X (2018) Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 362: 6416.

Moffitt JR, Zhuang X (2016) RNA imaging with multiplexed error-robust fluorescence in situ hybridization (MERFISH). Methods Enzymol 572: 1−49

Mu Q, Chen Y, Wang J (2019) Deciphering brain complexity using single-cell sequencing. Genom Proteom Bioinf 17(4): 344−366

Papp B, Plath K (2012) Pluripotency re-centered around Esrrb. EMBO J 31(22): 4255−4257

Peterson VM, Zhang KX, Kumar N, Wong J, Li L, Wilson DC, Moore R, McClanahan TK, Sadekova S, Klappenbach JA (2017) Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol 35(10): 936−939

Pogo BG, Allfrey VG, Mirsky AE (1966) RNA synthesis and histone acetylation during the course of gene activation in lymphocytes. Proc Natl Acad Sci USA 55(4): 805−812

Pollen AA, Nowakowski TJ, Shuga J, Wang X, Leyrat AA, Lui JH, Li N, Szpankowski L, Fowler B, Chen P, Ramalingam N, Sun G, Thu M, Norris M, Lebofsky R, Toppani D, Kemp DW, 2nd, Wong M, Clerkson B, Jones BN, Wu S, Knutsson L, Alvarado B, Wang J, Weaver LS, May AP, Jones RC, Unger MA, Kriegstein AR, West JA (2014) Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol 32(10): 1053−1058

Pott S (2017) Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells. Elife 6: e23203.

Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333): 279−283

Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5(10): 877−879

Regev A, Teichmann S, Lander E, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Participants H (2017) Science forum: the human cell atlas. ELife 6: e27041.

Reimegard J, Tarbier M, Danielsson M, Schuster J, Baskaran S, Panagiotou S, Dahl N, Friedlander MR, Gallant CJ (2021) A combined approach for single-cell mRNA and intracellular protein expression analysis. Commun Biol 4(1): 624.

Reyes M, Billman K, Hacohen N, Blainey PC (2019) Simultaneous profiling of gene expression and chromatin accessibility in single cells. Adv Biosyst 3: 11.

Rodriques SG, Stickels RR, Goeva A, Martin CA, Murray E, Vanderburg CR, Welch J, Chen LLM, Chen F, Macosko EZ (2019) Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363(6434): 1463−1467

Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE (2015) Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 33(11): 1165−1172

Rowley MJ, Corces VG (2016) The three-dimensional genome: principles and roles of long-distance interactions. Curr Opin Cell Biol 40: 8−14

Sahara S, O'Leary DD (2009) Fgf10 regulates transition period of cortical stem cell differentiation to radial glia controlling generation of neurons and basal progenitors. Neuron 63(1): 48−62

Schubeler D (2015) Function and information content of DNA methylation. Nature 517(7534): 321−326

Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L (2018) Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Cell 174(2): 363−376

Skene NG, Bryois J, Bakken TE, Breen G, Crowley JJ, Gaspar HA, Giusti-Rodriguez P, Hodge RD, Miller JA, Munoz-Manchado AB, O'Donovan MC, Owen MJ, Pardinas AF, Ryge J, Walters JTR, Linnarsson S, Lein ES, Major Depressive Disorder Working Group of the Psychiatric Genomics C, Sullivan PF, Hjerling-Leffler J (2018) Genetic identification of brain cell types underlying schizophrenia. Nat Genet 50(6): 825−833

Skene PJ, Henikoff S (2017) An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6: e21856.

Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C (2021) Embryo-scale, single-cell spatial transcriptomics. Science 373(6550): 111−117

Stadhouders R, Filion GJ, Graf T (2019) Transcription factors and 3D genome conformation in cell-fate decisions. Nature 569(7756): 345−354

Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T (2018) Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 50(2): 238−249

Stahl PL, Salmen F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg A, Ponten F, Costea PI, Sahlen P, Mulder J, Bergmann O, Lundeberg J, Frisen J (2016) Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353(6294): 78−82

Stickels RR, Murray E, Kumar P, Li J, Marshall JL, Di Bella DJ, Arlotta P, Macosko EZ, Chen F (2021) Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat Biotechnol 39(3): 313−319

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P (2017) Simultaneous epitope and transcriptome measurement in single cells. Nat Methods 14(9): 865−868

Tan SS, Valcanis H, Kalloniatis M, Harvey A (2002) Cellular dispersion patterns and phenotypes in the developing mouse superior colliculus. Dev Biol 241(1): 117−131

Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, Wang X, Bodeau J, Tuch BB, Siddiqui A, Lao K, Surani MA (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6(5): 377−382

Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H (2018) Shared and distinct transcriptomic cell types across neocortical areas. Nature 563(7729): 72−78

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee BK, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA (2012) The accessible chromatin landscape of the human genome. Nature 489(7414): 75−82

Trevino AE, Müller F, Andersen J, Sundaram L, Kathiria A, Shcherbina A, Farh K, Chang HY, Pașca AM, Kundaje A, Pașca SP, Greenleaf WJ (2021) Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution. Cell : S0092-8674(21)00942-9.

Vanlandewijck M, He L, Mae MA, Andrae J, Ando K, Del Gaudio F, Nahar K, Lebouvier T, Lavina B, Gouveia L, Sun Y, Raschperger E, Rasanen M, Zarb Y, Mochizuki N, Keller A, Lendahl U, Betsholtz C (2018) A molecular atlas of cell types and zonation in the brain vasculature. Nature 554(7693): 475−480

Vickovic S, Eraslan G, Salmen F, Klughammer J, Stenbeck L, Schapiro D, Aijo T, Bonneau R, Bergenstrahle L, Navarro JF, Gould J, Griffin GK, Borg A, Ronaghi M, Frisen J, Lundeberg J, Regev A, Stahl PL (2019) High-definition spatial transcriptomics for in situ tissue profiling. Nat Methods 16(10): 987−990

Wang QH, Xiong HQ, Ai SS, Yu XH, Liu YX, Zhang JJ, He AB (2019) CoBATCH for high-throughput single-cell epigenomic profiling. Molecular Cell 76(1): 206−216

Wang X, Allen WE, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C, Liu J, Nolan GP, Bava FA, Deisseroth K (2018) Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 361: 6400.

Wang Y, Yuan P, Yan Z, Yang M, Huo Y, Nie Y, Zhu X, Qiao J, Yan L (2021) Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos. Nat Commun 12(1): 1247.

Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10(1): 57−63

Watanabe Y, Sakuma C, Yaginuma H (2018) Dispersing movement of tangential neuronal migration in superficial layers of the developing chick optic tectum. Dev Biol 437(2): 131−139

Xiong H, Luo Y, Wang Q, Yu X, He A (2021) Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions. Nat Methods 18(6): 652−660

Zhang B, Kuster B (2019) Proteomics is not an island: multi-omics integration is the key to understanding biological systems. Mol Cell Proteomics 18(8 suppl 1): S1−S4

Zhu C, Preissl S, Ren B (2020) Single-cell multimodal omics: the power of many. Nat Methods 17(1): 11−14

Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R, Lucero J, Behrens MM, Hu M, Ren B (2019) An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat Struct Mol Biol 26(11): 1063−1070

Zhu C, Zhang Y, Li YE, Lucero J, Behrens MM, Ren B (2021) Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat Methods 18(3): 283−292

Publication history
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Publication history

Received: 30 July 2021
Accepted: 04 September 2021
Published: 24 November 2021
Issue date: June 2022


© The Author(s) 2022



This work was supported by the National Key Research and Development Program of China (2020YFA0112200)

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