{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T03:08:58Z","timestamp":1793761738088,"version":"4.6.1"},"reference-count":115,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T00:00:00Z","timestamp":1707436800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T00:00:00Z","timestamp":1707436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91953201"],"award-info":[{"award-number":["91953201"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21825701"],"award-info":[{"award-number":["21825701"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People\u2019s Republic of China","doi-asserted-by":"publisher","award":["2019YFA0110900"],"award-info":[{"award-number":["2019YFA0110900"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People\u2019s Republic of China","doi-asserted-by":"publisher","award":["2023YFC3402200"],"award-info":[{"award-number":["2023YFC3402200"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People\u2019s Republic of China","doi-asserted-by":"publisher","award":["2019YFA0802201"],"award-info":[{"award-number":["2019YFA0802201"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004826","name":"Natural Science Foundation of Beijing Municipality","doi-asserted-by":"publisher","award":["Z220013"],"award-info":[{"award-number":["Z220013"]}],"id":[{"id":"10.13039\/501100004826","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Biotechnol"],"published-print":{"date-parts":[[2025,1]]},"DOI":"10.1038\/s41587-024-02148-9","type":"journal-article","created":{"date-parts":[[2024,2,9]],"date-time":"2024-02-09T11:02:39Z","timestamp":1707476559000},"page":"85-96","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":51,"title":["Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq"],"prefix":"10.1038","volume":"43","author":[{"given":"Dongsheng","family":"Bai","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huifen","family":"Xiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zijian","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4216-6562","authenticated-orcid":false,"given":"Chenxu","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2540-9729","authenticated-orcid":false,"given":"Chengqi","family":"Yi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,2,9]]},"reference":[{"key":"2148_CR1","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1126\/science.aan6826","volume":"358","author":"G Kelsey","year":"2017","unstructured":"Kelsey, G., Stegle, O. & Reik, W. Single-cell epigenomics: recording the past and predicting the future. Science 358, 69\u201375 (2017).","journal-title":"Science"},{"key":"2148_CR2","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nrg.2016.83","volume":"17","author":"H Zhu","year":"2016","unstructured":"Zhu, H., Wang, G. & Qian, J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 17, 551\u2013565 (2016).","journal-title":"Nat. Rev. Genet."},{"key":"2148_CR3","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1016\/j.cell.2011.08.042","volume":"146","author":"N Bhutani","year":"2011","unstructured":"Bhutani, N., Burns, D. M. & Blau, H. M. DNA demethylation dynamics. Cell 146, 866\u2013872 (2011).","journal-title":"Cell"},{"key":"2148_CR4","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1038\/nrg.2017.33","volume":"18","author":"X Wu","year":"2017","unstructured":"Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517\u2013534 (2017).","journal-title":"Nat. Rev. Genet."},{"key":"2148_CR5","doi-asserted-by":"publisher","first-page":"1336","DOI":"10.1126\/science.aat6806","volume":"361","author":"C Luo","year":"2018","unstructured":"Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: in the right place at the right time. Science 361, 1336\u20131340 (2018).","journal-title":"Science"},{"key":"2148_CR6","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1038\/nrg3354","volume":"14","author":"ZD Smith","year":"2013","unstructured":"Smith, Z. D. & Meissner, A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 14, 204\u2013220 (2013).","journal-title":"Nat. Rev. Genet."},{"key":"2148_CR7","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1038\/s41576-018-0004-3","volume":"19","author":"S Horvath","year":"2018","unstructured":"Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371\u2013384 (2018).","journal-title":"Nat. Rev. Genet."},{"key":"2148_CR8","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/s41576-020-00287-8","volume":"22","author":"A Parry","year":"2021","unstructured":"Parry, A., Rulands, S. & Reik, W. Active turnover of DNA methylation during cell fate decisions. Nat. Rev. Genet. 22, 59\u201366 (2021).","journal-title":"Nat. Rev. Genet."},{"key":"2148_CR9","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1101\/gr.4074106","volume":"16","author":"GE Crawford","year":"2006","unstructured":"Crawford, G. E. et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16, 123\u2013131 (2006).","journal-title":"Genome Res."},{"key":"2148_CR10","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","volume":"10","author":"JD Buenrostro","year":"2013","unstructured":"Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213\u20131218 (2013).","journal-title":"Nat. Methods"},{"key":"2148_CR11","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1126\/science.1141319","volume":"316","author":"DS Johnson","year":"2007","unstructured":"Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein\u2013DNA interactions. Science 316, 1497\u20131502 (2007).","journal-title":"Science"},{"key":"2148_CR12","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nature08514","volume":"462","author":"R Lister","year":"2009","unstructured":"Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315\u2013322 (2009).","journal-title":"Nature"},{"key":"2148_CR13","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/s41586-020-2493-4","volume":"583","author":"EP Consortium","year":"2020","unstructured":"Consortium, E. P. et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699\u2013710 (2020).","journal-title":"Nature"},{"key":"2148_CR14","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/nmeth.1315","volume":"6","author":"F Tang","year":"2009","unstructured":"Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377\u2013382 (2009).","journal-title":"Nat. Methods"},{"key":"2148_CR15","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202\u20131214 (2015).","journal-title":"Cell"},{"key":"2148_CR16","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1016\/j.cell.2015.04.044","volume":"161","author":"AM Klein","year":"2015","unstructured":"Klein, A. M. et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161, 1187\u20131201 (2015).","journal-title":"Cell"},{"key":"2148_CR17","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nature12593","volume":"502","author":"T Nagano","year":"2013","unstructured":"Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59\u201364 (2013).","journal-title":"Nature"},{"key":"2148_CR18","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1038\/nature15740","volume":"528","author":"W Jin","year":"2015","unstructured":"Jin, W. et al. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature 528, 142\u2013146 (2015).","journal-title":"Nature"},{"key":"2148_CR19","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1126\/science.aab1601","volume":"348","author":"DA Cusanovich","year":"2015","unstructured":"Cusanovich, D. A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910\u2013914 (2015).","journal-title":"Science"},{"key":"2148_CR20","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/nature14590","volume":"523","author":"JD Buenrostro","year":"2015","unstructured":"Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486\u2013490 (2015).","journal-title":"Nature"},{"key":"2148_CR21","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1038\/s41593-018-0079-3","volume":"21","author":"S Preissl","year":"2018","unstructured":"Preissl, S. et al. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Nat. Neurosci. 21, 432\u2013439 (2018).","journal-title":"Nat. Neurosci."},{"key":"2148_CR22","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1038\/nbt.3383","volume":"33","author":"A Rotem","year":"2015","unstructured":"Rotem, A. et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165\u20131172 (2015).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR23","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1038\/s41556-018-0248-3","volume":"21","author":"A Harada","year":"2019","unstructured":"Harada, A. et al. A chromatin integration labelling method enables epigenomic profiling with lower input. Nat. Cell Biol. 21, 287\u2013296 (2019).","journal-title":"Nat. Cell Biol."},{"key":"2148_CR24","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09982-5","volume":"10","author":"HS Kaya-Okur","year":"2019","unstructured":"Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).","journal-title":"Nat. Commun."},{"key":"2148_CR25","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11559-1","volume":"10","author":"B Carter","year":"2019","unstructured":"Carter, B. et al. Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq). Nat. Commun. 10, 3747 (2019).","journal-title":"Nat. Commun."},{"key":"2148_CR26","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/s41592-019-0361-7","volume":"16","author":"WL Ku","year":"2019","unstructured":"Ku, W. L. et al. Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification. Nat. Methods 16, 323\u2013325 (2019).","journal-title":"Nat. Methods"},{"key":"2148_CR27","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.molcel.2019.07.015","volume":"76","author":"Q Wang","year":"2019","unstructured":"Wang, Q. et al. CoBATCH for high-throughput single-cell epigenomic profiling. Mol. Cell 76, 206\u2013216 (2019).","journal-title":"Mol. Cell"},{"key":"2148_CR28","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1038\/s41556-019-0383-5","volume":"21","author":"S Ai","year":"2019","unstructured":"Ai, S. et al. Profiling chromatin states using single-cell itChIP-seq. Nat. Cell Biol. 21, 1164\u20131172 (2019).","journal-title":"Nat. Cell Biol."},{"key":"2148_CR29","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1038\/s41588-019-0424-9","volume":"51","author":"K Grosselin","year":"2019","unstructured":"Grosselin, K. et al. High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer. Nat. Genet. 51, 1060\u20131066 (2019).","journal-title":"Nat. Genet."},{"key":"2148_CR30","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1101\/gr.161679.113","volume":"23","author":"H Guo","year":"2013","unstructured":"Guo, H. et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 23, 2126\u20132135 (2013).","journal-title":"Genome Res."},{"key":"2148_CR31","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/nbt.3598","volume":"34","author":"D Mooijman","year":"2016","unstructured":"Mooijman, D., Dey, S. S., Boisset, J. C., Crosetto, N. & van Oudenaarden, A. Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction. Nat. Biotechnol. 34, 852\u2013856 (2016).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR32","doi-asserted-by":"publisher","first-page":"720","DOI":"10.1016\/j.stem.2017.02.013","volume":"20","author":"C Zhu","year":"2017","unstructured":"Zhu, C. et al. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell 20, 720\u2013731 (2017).","journal-title":"Cell Stem Cell"},{"key":"2148_CR33","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1101\/gad.294843.116","volume":"31","author":"X Wu","year":"2017","unstructured":"Wu, X., Inoue, A., Suzuki, T. & Zhang, Y. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes Dev. 31, 511\u2013523 (2017).","journal-title":"Genes Dev."},{"key":"2148_CR34","doi-asserted-by":"publisher","first-page":"600","DOI":"10.1126\/science.aan3351","volume":"357","author":"C Luo","year":"2017","unstructured":"Luo, C. et al. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science 357, 600\u2013604 (2017).","journal-title":"Science"},{"key":"2148_CR35","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1038\/nbt.4038","volume":"36","author":"BB Lake","year":"2018","unstructured":"Lake, B. B. et al. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat. Biotechnol. 36, 70\u201380 (2018).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR36","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1126\/science.aau0730","volume":"361","author":"J Cao","year":"2018","unstructured":"Cao, J. et al. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science 361, 1380\u20131385 (2018).","journal-title":"Science"},{"key":"2148_CR37","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1038\/s41587-019-0290-0","volume":"37","author":"S Chen","year":"2019","unstructured":"Chen, S., Lake, B. B. & Zhang, K. High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat. Biotechnol. 37, 1452\u20131457 (2019).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR38","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1038\/s41594-019-0323-x","volume":"26","author":"C Zhu","year":"2019","unstructured":"Zhu, C. et al. An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat. Struct. Mol. Biol. 26, 1063\u20131070 (2019).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2148_CR39","doi-asserted-by":"crossref","unstructured":"Luo, C. et al. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity. Cell Genom. 2, 100107 (2022).","DOI":"10.1016\/j.xgen.2022.100107"},{"key":"2148_CR40","doi-asserted-by":"publisher","first-page":"1428","DOI":"10.1038\/s41594-023-01060-1","volume":"30","author":"Y Xie","year":"2023","unstructured":"Xie, Y. et al. Droplet-based single-cell joint profiling of histone modifications and transcriptomes. Nat. Struct. Mol. Biol. 30, 1428\u20131433 (2023).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2148_CR41","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1038\/nmeth.3035","volume":"11","author":"SA Smallwood","year":"2014","unstructured":"Smallwood, S. A. et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817\u2013820 (2014).","journal-title":"Nat. Methods"},{"key":"2148_CR42","doi-asserted-by":"publisher","first-page":"1386","DOI":"10.1016\/j.celrep.2015.02.001","volume":"10","author":"M Farlik","year":"2015","unstructured":"Farlik, M. et al. Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep. 10, 1386\u20131397 (2015).","journal-title":"Cell Rep."},{"key":"2148_CR43","doi-asserted-by":"publisher","first-page":"428\u2013431","DOI":"10.1038\/nbt.4112","volume":"36","author":"RM Mulqueen","year":"2018","unstructured":"Mulqueen, R. M. et al. Highly scalable generation of DNA methylation profiles in single cells. Nat. Biotechnol. 36, 428\u2013431 (2018).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-35374-3","volume":"13","author":"RV Nichols","year":"2022","unstructured":"Nichols, R. V. et al. High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nat. Commun. 13, 7627 (2022).","journal-title":"Nat. Commun."},{"key":"2148_CR45","doi-asserted-by":"publisher","first-page":"100060","DOI":"10.1016\/j.crmeth.2021.100060","volume":"1","author":"C Wangsanuwat","year":"2021","unstructured":"Wangsanuwat, C., Chialastri, A., Aldeguer, J. F., Rivron, N. C. & Dey, S. S. A probabilistic framework for cellular lineage reconstruction using integrated single-cell 5-hydroxymethylcytosine and genomic DNA sequencing. Cell Rep. Methods 1, 100060 (2021).","journal-title":"Cell Rep. Methods"},{"key":"2148_CR46","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.1016\/j.cell.2012.04.027","volume":"149","author":"M Yu","year":"2012","unstructured":"Yu, M. et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368\u20131380 (2012).","journal-title":"Cell"},{"key":"2148_CR47","doi-asserted-by":"publisher","first-page":"13190","DOI":"10.1021\/jacs.8b08297","volume":"140","author":"H Zeng","year":"2018","unstructured":"Zeng, H. et al. Bisulfite-free, nanoscale analysis of 5-hydroxymethylcytosine at single base resolution. J. Am. Chem. Soc. 140, 13190\u201313194 (2018).","journal-title":"J. Am. Chem. Soc."},{"key":"2148_CR48","doi-asserted-by":"publisher","unstructured":"Schutsky, E. K. et al. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/nbt.4204 (2018).","DOI":"10.1038\/nbt.4204"},{"key":"2148_CR49","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1016\/j.celrep.2013.01.001","volume":"3","author":"Z Sun","year":"2013","unstructured":"Sun, Z. et al. High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell Rep 3, 567\u2013576 (2013).","journal-title":"Cell Rep"},{"key":"2148_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-20920-2","volume":"12","author":"Y Liu","year":"2021","unstructured":"Liu, Y. et al. Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution. Nat. Commun. 12, 618 (2021).","journal-title":"Nat. Commun."},{"key":"2148_CR51","doi-asserted-by":"publisher","first-page":"11040","DOI":"10.1073\/pnas.1018448108","volume":"108","author":"D Cohen-Karni","year":"2011","unstructured":"Cohen-Karni, D. et al. The MspJI family of modification-dependent restriction endonucleases for epigenetic studies. Proc. Natl Acad. Sci. USA 108, 11040\u201311045 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2148_CR52","doi-asserted-by":"publisher","first-page":"1280","DOI":"10.1101\/gr.266551.120","volume":"31","author":"R Vaisvila","year":"2021","unstructured":"Vaisvila, R. et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res 31, 1280\u20131289 (2021).","journal-title":"Genome Res"},{"key":"2148_CR53","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-21532-6","volume":"12","author":"M Sen","year":"2021","unstructured":"Sen, M. et al. Strand-specific single-cell methylomics reveals distinct modes of DNA demethylation dynamics during early mammalian development. Nat. Commun. 12, 1286 (2021).","journal-title":"Nat. Commun."},{"key":"2148_CR54","unstructured":"Fullgrabe, J. et al. Simultaneous sequencing of genetic and epigenetic bases in DNA. Nat. Biotechnol. 41, 1457\u20131464 (2023)."},{"key":"2148_CR55","doi-asserted-by":"publisher","first-page":"424\u2013429","DOI":"10.1038\/s41587-019-0041-2","volume":"37","author":"YB Liu","year":"2019","unstructured":"Liu, Y. B. et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat. Biotechnol. 37, 424\u2013429 (2019).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR56","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1126\/science.1169786","volume":"324","author":"S Kriaucionis","year":"2009","unstructured":"Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929\u2013930 (2009).","journal-title":"Science"},{"key":"2148_CR57","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1126\/science.1220671","volume":"336","author":"MJ Booth","year":"2012","unstructured":"Booth, M. J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934\u2013937 (2012).","journal-title":"Science"},{"key":"2148_CR58","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1038\/nmeth.3569","volume":"12","author":"B Xia","year":"2015","unstructured":"Xia, B. et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat. Methods 12, 1047\u20131050 (2015).","journal-title":"Nat. Methods"},{"key":"2148_CR59","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1126\/science.1210597","volume":"333","author":"S Ito","year":"2011","unstructured":"Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300\u20131303 (2011).","journal-title":"Science"},{"key":"2148_CR60","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1126\/science.aam8999","volume":"360","author":"AB Rosenberg","year":"2018","unstructured":"Rosenberg, A. B. et al. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Science 360, 176\u2013182 (2018).","journal-title":"Science"},{"key":"2148_CR61","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/nmeth.2375","volume":"10","author":"T Daley","year":"2013","unstructured":"Daley, T. & Smith, A. D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325\u2013327 (2013).","journal-title":"Nat. Methods"},{"key":"2148_CR62","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1016\/j.stemcr.2017.04.001","volume":"8","author":"YJ Sim","year":"2017","unstructured":"Sim, Y. J. et al. 2i maintains a naive ground state in ESCs through two distinct epigenetic mechanisms. Stem Cell Rep. 8, 1312\u20131328 (2017).","journal-title":"Stem Cell Rep."},{"key":"2148_CR63","doi-asserted-by":"publisher","first-page":"4841","DOI":"10.1093\/nar\/gks155","volume":"40","author":"H Hashimoto","year":"2012","unstructured":"Hashimoto, H. et al. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 40, 4841\u20134849 (2012).","journal-title":"Nucleic Acids Res."},{"key":"2148_CR64","doi-asserted-by":"publisher","first-page":"1498","DOI":"10.1016\/j.cell.2011.11.054","volume":"147","author":"O Yildirim","year":"2011","unstructured":"Yildirim, O. et al. Mbd3\/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147, 1498\u20131510 (2011).","journal-title":"Cell"},{"key":"2148_CR65","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1038\/nmeth.4401","volume":"14","author":"AN Schep","year":"2017","unstructured":"Schep, A. N., Wu, B., Buenrostro, J. D. & Greenleaf, W. J. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat. Methods 14, 975\u2013978 (2017).","journal-title":"Nat. Methods"},{"key":"2148_CR66","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1016\/j.cell.2012.03.026","volume":"149","author":"H Marks","year":"2012","unstructured":"Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590\u2013604 (2012).","journal-title":"Cell"},{"key":"2148_CR67","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1101\/gad.1823109","volume":"23","author":"T Kobayashi","year":"2009","unstructured":"Kobayashi, T. et al. The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells. Genes Dev. 23, 1870\u20131875 (2009).","journal-title":"Genes Dev."},{"key":"2148_CR68","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/nn1131","volume":"6","author":"M Bylund","year":"2003","unstructured":"Bylund, M., Andersson, E., Novitch, B. G. & Muhr, J. Vertebrate neurogenesis is counteracted by Sox1\u20133 activity. Nat. Neurosci. 6, 1162\u20131168 (2003).","journal-title":"Nat. Neurosci."},{"key":"2148_CR69","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1016\/j.cell.2006.07.024","volume":"126","author":"K Takahashi","year":"2006","unstructured":"Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663\u2013676 (2006).","journal-title":"Cell"},{"key":"2148_CR70","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1016\/j.stem.2013.06.002","volume":"13","author":"E Habibi","year":"2013","unstructured":"Habibi, E. et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360\u2013369 (2013).","journal-title":"Cell Stem Cell"},{"key":"2148_CR71","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1126\/science.1170116","volume":"324","author":"M Tahiliani","year":"2009","unstructured":"Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930\u2013935 (2009).","journal-title":"Science"},{"key":"2148_CR72","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.1630","volume":"28","author":"CY McLean","year":"2010","unstructured":"McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495\u2013501 (2010).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR73","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1016\/j.cell.2013.02.004","volume":"152","author":"CG Spruijt","year":"2013","unstructured":"Spruijt, C. G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146\u20131159 (2013).","journal-title":"Cell"},{"key":"2148_CR74","doi-asserted-by":"crossref","unstructured":"Blondel, V. D., Guillaume, J. L., Lambiotte, R. & Lefebvre, E. Fast unfolding of communities in large networks. J. Stat. Mech. P10008 (2008).","DOI":"10.1088\/1742-5468\/2008\/10\/P10008"},{"key":"2148_CR75","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1084\/jem.20161046","volume":"214","author":"SA Nish","year":"2017","unstructured":"Nish, S. A. et al. CD4+ T cell effector commitment coupled to self-renewal by asymmetric cell divisions. J. Exp. Med. 214, 39\u201347 (2017).","journal-title":"J. Exp. Med."},{"key":"2148_CR76","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/2162-3619-1-36","volume":"1","author":"K Wang","year":"2012","unstructured":"Wang, K., Wei, G. & Liu, D. CD19: a biomarker for B cell development, lymphoma diagnosis and therapy. Exp. Hematol. Oncol. 1, 36 (2012).","journal-title":"Exp. Hematol. Oncol."},{"key":"2148_CR77","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1016\/j.cyto.2009.07.003","volume":"47","author":"CE Egwuagu","year":"2009","unstructured":"Egwuagu, C. E. STAT3 in CD4+ T helper cell differentiation and inflammatory diseases. Cytokine 47, 149\u2013156 (2009).","journal-title":"Cytokine"},{"key":"2148_CR78","doi-asserted-by":"publisher","first-page":"10735","DOI":"10.1073\/pnas.1306691110","volume":"110","author":"S Tsukumo","year":"2013","unstructured":"Tsukumo, S. et al. Bach2 maintains T cells in a naive state by suppressing effector memory-related genes. Proc. Natl Acad. Sci. USA 110, 10735\u201310740 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2148_CR79","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nmeth.1906","volume":"9","author":"J Ernst","year":"2012","unstructured":"Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215\u2013216 (2012).","journal-title":"Nat. Methods"},{"key":"2148_CR80","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1126\/science.1136352","volume":"315","author":"A Hellman","year":"2007","unstructured":"Hellman, A. & Chess, A. Gene body-specific methylation on the active X chromosome. Science 315, 1141\u20131143 (2007).","journal-title":"Science"},{"key":"2148_CR81","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r54","volume":"12","author":"H Stroud","year":"2011","unstructured":"Stroud, H., Feng, S., Morey Kinney, S., Pradhan, S. & Jacobsen, S. E. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 12, R54 (2011).","journal-title":"Genome Biol."},{"key":"2148_CR82","doi-asserted-by":"publisher","unstructured":"Fabyanic, E. B. et al. Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-022-01652-0 (2023).","DOI":"10.1038\/s41587-022-01652-0"},{"key":"2148_CR83","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1038\/s41592-021-01060-3","volume":"18","author":"C Zhu","year":"2021","unstructured":"Zhu, C. et al. Joint profiling of histone modifications and transcriptome in single cells from mouse brain. Nat. Methods 18, 283\u2013292 (2021).","journal-title":"Nat. Methods"},{"key":"2148_CR84","doi-asserted-by":"publisher","first-page":"10343","DOI":"10.1073\/pnas.0400768101","volume":"101","author":"FM Theriault","year":"2004","unstructured":"Theriault, F. M., Roy, P. & Stifani, S. AML1\/Runx1 is important for the development of hindbrain cholinergic branchiovisceral motor neurons and selected cranial sensory neurons. Proc. Natl Acad. Sci. USA 101, 10343\u201310348 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2148_CR85","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.ydbio.2017.10.019","volume":"432","author":"E Matuzelski","year":"2017","unstructured":"Matuzelski, E. et al. Transcriptional regulation of Nfix by NFIB drives astrocytic maturation within the developing spinal cord. Dev. Biol. 432, 286\u2013297 (2017).","journal-title":"Dev. Biol."},{"key":"2148_CR86","doi-asserted-by":"publisher","first-page":"eadi0197","DOI":"10.1126\/sciadv.adi0197","volume":"9","author":"R Viswanathan","year":"2023","unstructured":"Viswanathan, R. et al. DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA. Sci. Adv. 9, eadi0197 (2023).","journal-title":"Sci. Adv."},{"key":"2148_CR87","doi-asserted-by":"publisher","unstructured":"Chialastri, A., Sarkar, S., Schauer, E. E., Lamba, S. & Dey, S. S. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2023.05.06.539708 (2023).","DOI":"10.1101\/2023.05.06.539708"},{"key":"2148_CR88","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1186\/s13287-018-1099-3","volume":"9","author":"HM Shahjalal","year":"2018","unstructured":"Shahjalal, H. M., Abdal Dayem, A., Lim, K. M., Jeon, T. I. & Cho, S. G. Generation of pancreatic \u03b2 cells for treatment of diabetes: advances and challenges. Stem Cell Res. Ther. 9, 355 (2018).","journal-title":"Stem Cell Res. Ther."},{"key":"2148_CR89","doi-asserted-by":"publisher","first-page":"916","DOI":"10.1038\/s41587-019-0147-6","volume":"37","author":"CA Lareau","year":"2019","unstructured":"Lareau, C. A. et al. Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nat. Biotechnol. 37, 916\u2013924 (2019).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR90","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/s41592-021-01153-z","volume":"18","author":"P Datlinger","year":"2021","unstructured":"Datlinger, P. et al. Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing. Nat. Methods 18, 635\u2013642 (2021).","journal-title":"Nat. Methods"},{"key":"2148_CR91","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1038\/nmeth.4380","volume":"14","author":"M Stoeckius","year":"2017","unstructured":"Stoeckius, M. et al. Simultaneous epitope and transcriptome measurement in single cells. Nat. Methods 14, 865\u2013868 (2017).","journal-title":"Nat. Methods"},{"key":"2148_CR92","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1038\/s41592-019-0502-z","volume":"16","author":"G Li","year":"2019","unstructured":"Li, G. et al. Joint profiling of DNA methylation and chromatin architecture in single cells. Nat. Methods 16, 991\u2013993 (2019).","journal-title":"Nat. Methods"},{"key":"2148_CR93","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1038\/s41592-019-0547-z","volume":"16","author":"DS Lee","year":"2019","unstructured":"Lee, D. S. et al. Simultaneous profiling of 3D genome structure and DNA methylation in single human cells. Nat. Methods 16, 999\u20131006 (2019).","journal-title":"Nat. Methods"},{"key":"2148_CR94","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1038\/s41587-021-00927-2","volume":"39","author":"EP Mimitou","year":"2021","unstructured":"Mimitou, E. P. et al. Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells. Nat. Biotechnol. 39, 1246\u20131258 (2021).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR95","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1038\/s41592-021-01278-1","volume":"18","author":"H Chung","year":"2021","unstructured":"Chung, H. et al. Joint single-cell measurements of nuclear proteins and RNA in vivo. Nat. Methods 18, 1204\u20131212 (2021).","journal-title":"Nat. Methods"},{"key":"2148_CR96","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1038\/s41587-022-01250-0","volume":"40","author":"B Zhang","year":"2022","unstructured":"Zhang, B. et al. Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. Nat. Biotechnol. 40, 1220\u20131230 (2022).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR97","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1038\/s41592-022-01461-y","volume":"19","author":"AF Chen","year":"2022","unstructured":"Chen, A. F. et al. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. Nat. Methods 19, 547\u2013553 (2022).","journal-title":"Nat. Methods"},{"key":"2148_CR98","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","volume":"184","author":"Y Hao","year":"2021","unstructured":"Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573\u20133587 (2021).","journal-title":"Cell"},{"key":"2148_CR99","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14976-9","volume":"11","author":"P Qiu","year":"2020","unstructured":"Qiu, P. Embracing the dropouts in single-cell RNA-seq analysis. Nat. Commun. 11, 1169 (2020).","journal-title":"Nat. Commun."},{"key":"2148_CR100","doi-asserted-by":"publisher","first-page":"7095","DOI":"10.1021\/jacs.3c01663","volume":"145","author":"H Xu","year":"2023","unstructured":"Xu, H. et al. Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine. J. Am. Chem. Soc. 145, 7095\u20137100 (2023).","journal-title":"J. Am. Chem. Soc."},{"key":"2148_CR101","doi-asserted-by":"publisher","first-page":"14508","DOI":"10.1073\/pnas.1208715109","volume":"109","author":"MW Schmitt","year":"2012","unstructured":"Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508\u201314513 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2148_CR102","doi-asserted-by":"publisher","first-page":"18761","DOI":"10.1073\/pnas.1313995110","volume":"110","author":"KC Chan","year":"2013","unstructured":"Chan, K. C. et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc. Natl Acad. Sci. USA 110, 18761\u201318768 (2013).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2148_CR103","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1038\/cr.2017.106","volume":"27","author":"CX Song","year":"2017","unstructured":"Song, C. X. et al. 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Res. 27, 1231\u20131242 (2017).","journal-title":"Cell Res."},{"key":"2148_CR104","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).","journal-title":"Genome Biol."},{"key":"2148_CR105","unstructured":"Krueger, F. Trim Galore. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/ (2019)."},{"key":"2148_CR106","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"2148_CR107","doi-asserted-by":"publisher","first-page":"861","DOI":"10.21105\/joss.00861","volume":"3","author":"L McInnes","year":"2008","unstructured":"McInnes, L., Healy, J., Saul, N. & Gro\u00dfberger, L. UMAP: uniform manifold approximation and projection. J. Open Source Softw. 3, 861 (2008).","journal-title":"J. Open Source Softw."},{"key":"2148_CR108","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.3192","volume":"33","author":"R Satija","year":"2015","unstructured":"Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495\u2013502 (2015).","journal-title":"Nat. Biotechnol."},{"key":"2148_CR109","doi-asserted-by":"crossref","unstructured":"Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379\u2013423 (1948).","DOI":"10.1002\/j.1538-7305.1948.tb01338.x"},{"key":"2148_CR110","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","volume":"566","author":"J Cao","year":"2019","unstructured":"Cao, J. et al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496\u2013502 (2019).","journal-title":"Nature"},{"key":"2148_CR111","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","volume":"38","author":"S Heinz","year":"2010","unstructured":"Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576\u2013589 (2010).","journal-title":"Mol. Cell"},{"key":"2148_CR112","doi-asserted-by":"crossref","unstructured":"Sherman, B. T. et al. DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update). Nucleic Acids Res. 50, W216\u2013W221 (2022).","DOI":"10.1093\/nar\/gkac194"},{"key":"2148_CR113","unstructured":"Bai, D., Zhu, C. & Yi, C. Single-cell joint analysis of 5-methylcytosine and 5-hydroxymethylcytosine. https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE197740 (2023)."},{"key":"2148_CR114","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1016\/j.stem.2015.09.011","volume":"17","author":"AA Kolodziejczyk","year":"2015","unstructured":"Kolodziejczyk, A. A. et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17, 471\u2013485 (2015).","journal-title":"Cell Stem Cell"},{"key":"2148_CR115","unstructured":"Bai, D., Zhu, C. & Yi, C. Custom scripts and pipeline for SIMPLE-seq data analysis. https:\/\/github.com\/cxzhu\/SIMPLE-seq (2023)."}],"container-title":["Nature Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41587-024-02148-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-024-02148-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41587-024-02148-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,16]],"date-time":"2025-01-16T23:02:45Z","timestamp":1737068565000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41587-024-02148-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,9]]},"references-count":115,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1]]}},"alternative-id":["2148"],"URL":"https:\/\/doi.org\/10.1038\/s41587-024-02148-9","relation":{},"ISSN":["1087-0156","1546-1696"],"issn-type":[{"value":"1087-0156","type":"print"},{"value":"1546-1696","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,2,9]]},"assertion":[{"value":"24 August 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 January 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 February 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}