{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T05:22:50Z","timestamp":1772688170423,"version":"3.50.1"},"reference-count":104,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2023,11,1]],"date-time":"2023-11-01T00:00:00Z","timestamp":1698796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20220279"],"award-info":[{"award-number":["BK20220279"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2021-I2M-1-061"],"award-info":[{"award-number":["2021-I2M-1-061"]}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["2022-I2M-2-004"],"award-info":[{"award-number":["2022-I2M-2-004"]}]},{"DOI":"10.13039\/501100005150","name":"Chinese Academy of Medical Sciences","doi-asserted-by":"publisher","award":["2022-RC416-01"],"award-info":[{"award-number":["2022-RC416-01"]}],"id":[{"id":"10.13039\/501100005150","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Suzhou Municipal Key Laboratory","award":["SZS2022005"],"award-info":[{"award-number":["SZS2022005"]}]},{"name":"Gusu Innovation and Entrepreneurship Leading Talents Program","award":["ZXL2022475"],"award-info":[{"award-number":["ZXL2022475"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The nervous system is one of the most complicated and enigmatic systems within the animal kingdom. Recently, the emergence and development of spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) technologies have provided an unprecedented ability to systematically decipher the cellular heterogeneity and spatial locations of the nervous system from multiple unbiased aspects. However, efficiently integrating, presenting and analyzing massive multiomic data remains a huge challenge. Here, we manually collected and comprehensively analyzed high-quality scRNA-seq and ST data from the nervous system, covering 10 679 684 cells. In addition, multi-omic\u00a0datasets from more than 900 species were included for extensive data mining from an evolutionary perspective. Furthermore, over 100 neurological diseases (e.g. Alzheimer's disease, Parkinson's disease, Down syndrome) were systematically analyzed for high-throughput screening of putative biomarkers. Differential expression patterns across developmental time points, cell types and ST spots were discerned and subsequently subjected to extensive interpretation. To provide researchers with efficient data exploration, we created a new database with interactive interfaces and integrated functions called the Spatiotemporal Cloud Atlas for Neural cells (SCAN), freely accessible at http:\/\/47.98.139.124:8799 or http:\/\/scanatlas.net. SCAN will benefit the neuroscience research community to better exploit the spatiotemporal atlas of the neural system and promote the development of diagnostic strategies for various neurological disorders.<\/jats:p>","DOI":"10.1093\/nar\/gkad895","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T17:16:45Z","timestamp":1699291005000},"page":"D998-D1009","source":"Crossref","is-referenced-by-count":8,"title":["SCAN: Spatiotemporal Cloud Atlas for Neural cells"],"prefix":"10.1093","volume":"52","author":[{"given":"Yushan","family":"Deng","sequence":"first","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yubao","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University , Guangzhou 510630 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengrou","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"},{"name":"Institutes of Biology and Medical Sciences (IBMS), Soochow University , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiayi","family":"Shen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"},{"name":"Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University , Yantai 264003 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5844-2616","authenticated-orcid":false,"given":"Siying","family":"Qin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6876-3173","authenticated-orcid":false,"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University , Guangzhou 510630 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiang","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhaoyang","family":"Shen","sequence":"additional","affiliation":[{"name":"Life Sciences and Technology College, China Pharmaceutical University , Nanjing 211198 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Changxiao","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tengfei","family":"Jia","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"},{"name":"Institutes of Biology and Medical Sciences (IBMS), Soochow University , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peixin","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"},{"name":"Cam-Su Genomic Resource Center, Medical College of Soochow University , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingmin","family":"Peng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yangfeng","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wensheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Peninsula Cancer Research Center, School of Basic Medical Sciences, Binzhou Medical University , Yantai 264003 , China"},{"name":"Cam-Su Genomic Resource Center, Medical College of Soochow University , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hebin","family":"Liu","sequence":"additional","affiliation":[{"name":"Institutes of Biology and Medical Sciences (IBMS), Soochow University , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangming","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University , Guangzhou 510630 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Limin","family":"Rong","sequence":"additional","affiliation":[{"name":"Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University , Guangzhou 510630 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangdong","family":"Wang","sequence":"additional","affiliation":[{"name":"Zhongshan Hospital, Department of Pulmonary and Critical Care Medicine, Institute for Clinical Science, Shanghai Institute of Clinical Bioinformatics , Shanghai 200000 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7196-4136","authenticated-orcid":false,"given":"Dongsheng","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,11,1]]},"reference":[{"key":"2024010511442672100_B1","doi-asserted-by":"crossref","first-page":"1186","DOI":"10.1038\/s41467-021-21453-4","article-title":"Optimal marker gene selection for cell type discrimination in single cell analyses","volume":"12","author":"Dumitrascu","year":"2021","journal-title":"Nat. Commun."},{"key":"2024010511442672100_B2","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat. Protoc."},{"key":"2024010511442672100_B3","doi-asserted-by":"crossref","first-page":"4768","DOI":"10.1038\/s41467-018-07165-2","article-title":"A web server for comparative analysis of single-cell RNA-seq data","volume":"9","author":"Alavi","year":"2018","journal-title":"Nat. Commun."},{"key":"2024010511442672100_B4","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41592-021-01171-x","article-title":"The triumphs and limitations of computational methods for scRNA-seq","volume":"18","author":"Kharchenko","year":"2021","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B5","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg3832","article-title":"Spatially resolved transcriptomics and beyond","volume":"16","author":"Crosetto","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"2024010511442672100_B6","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1126\/science.aan6827","article-title":"The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing","volume":"358","author":"Lein","year":"2017","journal-title":"Science"},{"key":"2024010511442672100_B7","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","article-title":"Exploring tissue architecture using spatial transcriptomics","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"2024010511442672100_B8","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1038\/s41587-021-01182-1","article-title":"Spatial components of molecular tissue biology","volume":"40","author":"Palla","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"2024010511442672100_B9","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/s41592-022-01409-2","article-title":"Museum of spatial transcriptomics","volume":"19","author":"Moses","year":"2022","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B10","article-title":"SCAR: Single-cell and Spatially-resolved Cancer Resources","author":"Deng","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B11","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/s41587-022-01448-2","article-title":"The expanding vistas of spatial transcriptomics","volume":"41","author":"Tian","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2024010511442672100_B12","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/s12929-022-00879-y","article-title":"Spatial multi-omics analyses of the tumor immune microenvironment","volume":"29","author":"Hsieh","year":"2022","journal-title":"J. Biomed. Sci."},{"key":"2024010511442672100_B13","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1038\/s41576-021-00370-8","article-title":"Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics","volume":"22","author":"Longo","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"2024010511442672100_B14","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1038\/s41467-023-36707-6","article-title":"Spatial transcriptomics reveals niche-specific enrichment and vulnerabilities of radial glial stem-like cells in malignant gliomas","volume":"14","author":"Ren","year":"2023","journal-title":"Nat. Commun."},{"key":"2024010511442672100_B15","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/s41588-023-01435-6","article-title":"Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis","volume":"55","author":"Sampath\u00a0Kumar","year":"2023","journal-title":"Nat. Genet."},{"key":"2024010511442672100_B16","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"2024010511442672100_B17","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1016\/j.devcel.2022.04.009","article-title":"Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis","volume":"57","author":"Liu","year":"2022","journal-title":"Dev. Cell"},{"key":"2024010511442672100_B18","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1016\/j.devcel.2022.04.006","article-title":"High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae","volume":"57","author":"Wang","year":"2022","journal-title":"Dev. Cell"},{"key":"2024010511442672100_B19","doi-asserted-by":"crossref","first-page":"eabp9444","DOI":"10.1126\/science.abp9444","article-title":"Single-cell stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration","volume":"377","author":"Wei","year":"2022","journal-title":"Science"},{"key":"2024010511442672100_B20","doi-asserted-by":"crossref","first-page":"3726","DOI":"10.1016\/j.cell.2023.06.009","article-title":"Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex","volume":"186","author":"Chen","year":"2023","journal-title":"Cell"},{"key":"2024010511442672100_B21","doi-asserted-by":"crossref","first-page":"6747","DOI":"10.1038\/s41467-022-34413-3","article-title":"Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex","volume":"13","author":"Lei","year":"2022","journal-title":"Nat. Commun."},{"key":"2024010511442672100_B22","doi-asserted-by":"crossref","first-page":"368","DOI":"10.3390\/genes8120368","article-title":"scRNASeqDB: a database for RNA-seq based gene expression profiles in Human single cells","volume":"8","author":"Cao","year":"2017","journal-title":"Genes"},{"key":"2024010511442672100_B23","doi-asserted-by":"crossref","first-page":"4578","DOI":"10.1093\/bioinformatics\/btab503","article-title":"UCSC Cell Browser: visualize your single-cell data","volume":"37","author":"Speir","year":"2021","journal-title":"Bioinformatics"},{"key":"2024010511442672100_B24","doi-asserted-by":"crossref","first-page":"D129","DOI":"10.1093\/nar\/gkab1030","article-title":"Expression Atlas update: gene and protein expression in multiple species","volume":"50","author":"Moreno","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B25","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/s41586-020-2157-4","article-title":"Construction of a human cell landscape at single-cell level","volume":"581","author":"Han","year":"2020","journal-title":"Nature"},{"key":"2024010511442672100_B26","doi-asserted-by":"crossref","first-page":"D934","DOI":"10.1093\/nar\/gkab894","article-title":"VThunter: a database for single-cell screening of virus target cells in the animal kingdom","volume":"50","author":"Chen","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B27","doi-asserted-by":"crossref","first-page":"D125","DOI":"10.1093\/nar\/gkaa1017","article-title":"LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution","volume":"49","author":"Wang","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B28","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1681\/ASN.2021081150","article-title":"Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model","volume":"33","author":"Dixon","year":"2022","journal-title":"J. Am. Soc. Nephrol."},{"key":"2024010511442672100_B29","doi-asserted-by":"crossref","first-page":"D900","DOI":"10.1093\/nar\/gky939","article-title":"CancerSEA: a cancer single-cell state atlas","volume":"47","author":"Yuan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B30","doi-asserted-by":"crossref","first-page":"D1425","DOI":"10.1093\/nar\/gkac959","article-title":"TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment","volume":"51","author":"Han","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B31","doi-asserted-by":"crossref","first-page":"D781","DOI":"10.1093\/nar\/gkx949","article-title":"SCPortalen: human and mouse single-cell centric database","volume":"46","author":"Abugessaisa","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B32","doi-asserted-by":"crossref","first-page":"baz046","DOI":"10.1093\/database\/baz046","article-title":"PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data","volume":"2019","author":"Franz\u00e9n","year":"2019","journal-title":"Database"},{"key":"2024010511442672100_B33","doi-asserted-by":"crossref","first-page":"3375","DOI":"10.4049\/jimmunol.1700272","article-title":"JingleBells: a repository of immune-related single-cell RNA\u2013Sequencing datasets","volume":"198","author":"Ner-Gaon","year":"2017","journal-title":"J. Immunol."},{"key":"2024010511442672100_B34","doi-asserted-by":"crossref","first-page":"D1150","DOI":"10.1093\/nar\/gkac930","article-title":"SPEED: single-cell pan-species atlas in the light of ecology and evolution for development and diseases","volume":"51","author":"Chen","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B35","doi-asserted-by":"crossref","first-page":"bbaa325","DOI":"10.1093\/bib\/bbaa325","article-title":"ColorCells: a database of expression, classification and functions of lncRNAs in single cells","volume":"22","author":"Zheng","year":"2021","journal-title":"Brief. Bioinform."},{"key":"2024010511442672100_B36","doi-asserted-by":"crossref","first-page":"D1029","DOI":"10.1093\/nar\/gkaa762","article-title":"STAB: a spatio-temporal cell atlas of the human brain","volume":"49","author":"Song","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B37","doi-asserted-by":"crossref","first-page":"101769","DOI":"10.1016\/j.isci.2020.101769","article-title":"scREAD: a single-cell RNA-seq database for Alzheimer's disease","volume":"23","author":"Jiang","year":"2020","journal-title":"IScience"},{"key":"2024010511442672100_B38","doi-asserted-by":"crossref","first-page":"108204","DOI":"10.1016\/j.exer.2020.108204","article-title":"Spectacle: an interactive resource for ocular single-cell RNA sequencing data analysis","volume":"200","author":"Voigt","year":"2020","journal-title":"Exp. Eye Res."},{"key":"2024010511442672100_B39","doi-asserted-by":"crossref","first-page":"giab061","DOI":"10.1093\/gigascience\/giab061","article-title":"Building the mega single-cell transcriptome ocular meta-atlas","volume":"10","author":"Swamy","year":"2021","journal-title":"GigaScience"},{"key":"2024010511442672100_B40","doi-asserted-by":"crossref","first-page":"D1413","DOI":"10.1093\/nar\/gkaa838","article-title":"SC2disease: a manually curated database of single-cell transcriptome for human diseases","volume":"49","author":"Zhao","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B41","first-page":"D233","article-title":"SpatialDB: a database for spatially resolved transcriptomes","volume":"48","author":"Fan","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B42","doi-asserted-by":"crossref","DOI":"10.1101\/2022.03.11.481421","article-title":"STOmicsDB: a database of spatial transcriptomic data","author":"Xu","year":"2022"},{"key":"2024010511442672100_B43","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/s41592-023-01773-7","article-title":"SODB facilitates comprehensive exploration of spatial omics data","volume":"20","author":"Yuan","year":"2023","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B44","doi-asserted-by":"crossref","first-page":"D827","DOI":"10.1093\/nar\/gkac874","article-title":"Aquila: a spatial omics database and analysis platform","volume":"51","author":"Zheng","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B45","doi-asserted-by":"crossref","first-page":"W560","DOI":"10.1093\/nar\/gkad419","article-title":"STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data","volume":"51","author":"Li","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B46","doi-asserted-by":"crossref","first-page":"D1138","DOI":"10.1093\/nar\/gkac889","article-title":"SPASCER: spatial transcriptomics annotation at single-cell resolution","volume":"51","author":"Fan","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B47","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"NCBI GEO: archive for functional genomics data sets\u2014update","volume":"41","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B48","doi-asserted-by":"crossref","first-page":"D9","DOI":"10.1093\/nar\/gkac1098","article-title":"EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022","volume":"51","author":"Thakur","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B49","doi-asserted-by":"crossref","first-page":"eaba7721","DOI":"10.1126\/science.aba7721","article-title":"A human cell atlas of fetal gene expression","volume":"370","author":"Cao","year":"2020","journal-title":"Science"},{"key":"2024010511442672100_B50","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","article-title":"The single-cell transcriptional landscape of mammalian organogenesis","volume":"566","author":"Cao","year":"2019","journal-title":"Nature"},{"key":"2024010511442672100_B51","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1007\/s11427-022-2293-4","article-title":"FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome","volume":"66","author":"Guo","year":"2023","journal-title":"Sci. China Life Sci."},{"key":"2024010511442672100_B52","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2024010511442672100_B53","doi-asserted-by":"crossref","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"The Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2024010511442672100_B54","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2024010511442672100_B55","first-page":"100141","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"2024010511442672100_B56","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B57","doi-asserted-by":"crossref","first-page":"3374","DOI":"10.1093\/bioinformatics\/btab209","article-title":"ShinyCell: simple and sharable visualization of single-cell gene expression data","volume":"37","author":"Ouyang","year":"2021","journal-title":"Bioinformatics"},{"key":"2024010511442672100_B58","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"2024010511442672100_B59","doi-asserted-by":"crossref","first-page":"56","DOI":"10.25080\/Majora-92bf1922-00a","article-title":"Data structures for statistical computing in python","volume-title":"Proceedings of the 9th Python in Science Conference","author":"McKinney","year":"2010"},{"key":"2024010511442672100_B60","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.journal."},{"key":"2024010511442672100_B61","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2024010511442672100_B62","doi-asserted-by":"crossref","first-page":"D988","DOI":"10.1093\/nar\/gkab1049","article-title":"Ensembl 2022","volume":"50","author":"Cunningham","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B63","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2024010511442672100_B64","doi-asserted-by":"crossref","first-page":"W175","DOI":"10.1093\/nar\/gkac199","article-title":"ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and bisulfite-seq data","volume":"50","author":"Zou","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B65","doi-asserted-by":"crossref","first-page":"eaba7612","DOI":"10.1126\/science.aba7612","article-title":"A human cell atlas of fetal chromatin accessibility","volume":"370","author":"Domcke","year":"2020","journal-title":"Science"},{"key":"2024010511442672100_B66","doi-asserted-by":"crossref","first-page":"eabb8795","DOI":"10.1126\/science.abb8795","article-title":"A latent lineage potential in resident neural stem cells enables spinal cord repair","volume":"370","author":"Llorens-Bobadilla","year":"2020","journal-title":"Science"},{"key":"2024010511442672100_B67","doi-asserted-by":"crossref","first-page":"D88","DOI":"10.1093\/nar\/gkl822","article-title":"VISTA Enhancer browser\u2013a database of tissue-specific human enhancers","volume":"35","author":"Visel","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B68","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2024010511442672100_B69","doi-asserted-by":"crossref","first-page":"D882","DOI":"10.1093\/nar\/gkz1062","article-title":"New developments on the Encyclopedia of DNA Elements (ENCODE) data portal","volume":"48","author":"Luo","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B70","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1101\/gr.253492.119","article-title":"Identification and dynamic quantification of regulatory elements using total RNA","volume":"29","author":"Duttke","year":"2019","journal-title":"Genome Res."},{"key":"2024010511442672100_B71","doi-asserted-by":"crossref","first-page":"2247","DOI":"10.1038\/s41596-020-0336-2","article-title":"A scalable SCENIC workflow for single-cell gene regulatory network analysis","volume":"15","author":"Van\u00a0de\u00a0Sande","year":"2020","journal-title":"Nat. Protoc."},{"key":"2024010511442672100_B72","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell-cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"2024010511442672100_B73","first-page":"1695","article-title":"The igraph software package for complex network research","volume":"Complex Systems","author":"Cs\u00e1rdi","year":"2006","journal-title":"InterJournal"},{"key":"2024010511442672100_B74","article-title":"igraph: Network Analysis and Visualization in R","author":"Cs\u00e1rdi","year":"2023"},{"key":"2024010511442672100_B75","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2024010511442672100_B76","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1126\/science.aax0249","article-title":"Single-cell transcriptional diversity is a hallmark of developmental potential","volume":"367","author":"Gulati","year":"2020","journal-title":"Science"},{"key":"2024010511442672100_B77","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B78","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1016\/j.gpb.2021.04.001","article-title":"Genome Warehouse: a public repository housing Genome-scale data","volume":"19","author":"Chen","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2024010511442672100_B79","doi-asserted-by":"crossref","first-page":"D18","DOI":"10.1093\/nar\/gkac1073","article-title":"Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2023","volume":"51","author":"CNCB-NGDC Members and Partners","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B80","doi-asserted-by":"crossref","first-page":"D165","DOI":"10.1093\/nar\/gkab1113","article-title":"JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles","volume":"50","author":"Castro-Mondragon","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B81","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B82","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B83","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal Omega for making accurate alignments of many protein sequences: clustal Omega for many protein sequences","volume":"27","author":"Sievers","year":"2018","journal-title":"Protein Sci."},{"key":"2024010511442672100_B84","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2024010511442672100_B85","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1158\/2159-8290.CD-21-0316","article-title":"Spatiotemporal immune landscape of colorectal cancer liver metastasis at single-cell level","volume":"12","author":"Wu","year":"2022","journal-title":"Cancer Discov."},{"key":"2024010511442672100_B86","doi-asserted-by":"crossref","DOI":"10.1101\/2022.05.30.494067","article-title":"MEBOCOST: metabolite-mediated cell communication modeling by single cell transcriptome bioinformatics","author":"Zheng","year":"2022"},{"key":"2024010511442672100_B87","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B88","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"key":"2024010511442672100_B89","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.4636","article-title":"SpatialDE: identification of spatially variable genes","volume":"15","author":"Svensson","year":"2018","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B90","doi-asserted-by":"crossref","first-page":"eabl5197","DOI":"10.1126\/science.abl5197","article-title":"Cross-tissue immune cell analysis reveals tissue-specific features in humans","volume":"376","author":"Dom\u00ednguez\u00a0Conde","year":"2022","journal-title":"Science"},{"key":"2024010511442672100_B91","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1038\/s41593-019-0539-4","article-title":"A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation","volume":"22","author":"Grubman","year":"2019","journal-title":"Nat. Neurosci."},{"key":"2024010511442672100_B92","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.celrep.2019.03.099","article-title":"The major risk factors for Alzheimer's Disease: age, sex, and genes modulate the microglia response to a\u03b2 plaques","volume":"27","author":"Sala\u00a0Frigerio","year":"2019","journal-title":"Cell Rep."},{"key":"2024010511442672100_B93","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.celrep.2017.09.039","article-title":"Temporal tracking of microglia activation in neurodegeneration at single-cell resolution","volume":"21","author":"Mathys","year":"2017","journal-title":"Cell Rep."},{"key":"2024010511442672100_B94","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","article-title":"A unique microglia type associated with restricting development of Alzheimer's disease","volume":"169","author":"Keren-Shaul","year":"2017","journal-title":"Cell"},{"key":"2024010511442672100_B95","doi-asserted-by":"crossref","first-page":"134","DOI":"10.3389\/fnmol.2020.00134","article-title":"Profiling microglia from Alzheimer's Disease donors and non-demented elderly in acute Human postmortem cortical tissue","volume":"13","author":"Alsema","year":"2020","journal-title":"Front. Mol. Neurosci."},{"key":"2024010511442672100_B96","doi-asserted-by":"crossref","first-page":"645666","DOI":"10.3389\/fimmu.2021.645666","article-title":"Single-cell RNA sequencing of peripheral blood reveals immune cell signatures in Alzheimer's disease","volume":"12","author":"Xu","year":"2021","journal-title":"Front. Immunol."},{"key":"2024010511442672100_B97","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41586-021-03929-x","article-title":"Blood and immune development in human fetal bone marrow and Down syndrome","volume":"598","author":"Jardine","year":"2021","journal-title":"Nature"},{"key":"2024010511442672100_B98","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1038\/s41592-022-01480-9","article-title":"Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution","volume":"19","author":"Li","year":"2022","journal-title":"Nat. Methods"},{"key":"2024010511442672100_B99","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2024010511442672100_B100","doi-asserted-by":"crossref","first-page":"D1074","DOI":"10.1093\/nar\/gkx1037","article-title":"DrugBank 5.0: a major update to the DrugBank database for 2018","volume":"46","author":"Wishart","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B101","doi-asserted-by":"crossref","first-page":"D668","DOI":"10.1093\/nar\/gkj067","article-title":"DrugBank: a comprehensive resource for in silico drug discovery and exploration","volume":"34","author":"Wishart","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2024010511442672100_B102","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","article-title":"A next generation connectivity map: L1000 platform and the first 1,000,000 profiles","volume":"171","author":"Subramanian","year":"2017","journal-title":"Cell"},{"key":"2024010511442672100_B103","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1126\/science.aav9776","article-title":"Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis","volume":"364","author":"Maniatis","year":"2019","journal-title":"Science"},{"key":"2024010511442672100_B104","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/brain\/awab446","article-title":"Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state","volume":"145","author":"Smaji\u0107","year":"2022","journal-title":"Brain"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/D1\/D998\/55040609\/gkad895.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/52\/D1\/D998\/55040609\/gkad895.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,5]],"date-time":"2024-01-05T12:15:04Z","timestamp":1704456904000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/52\/D1\/D998\/7335755"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,1]]},"references-count":104,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2023,11,1]]},"published-print":{"date-parts":[[2024,1,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad895","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,5]]},"published":{"date-parts":[[2023,11,1]]}}}