{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T09:54:02Z","timestamp":1790502842769,"version":"4.1.0"},"reference-count":19,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,11,28]],"date-time":"2020-11-28T00:00:00Z","timestamp":1606521600000},"content-version":"vor","delay-in-days":332,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"A COMPREHENSIVE WHOLE-BRAIN ATLAS OF CELL TYPES IN THE MOUSE","award":["NIH U19MH114830"],"award-info":[{"award-number":["NIH U19MH114830"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The more than 1000 single-cell transcriptomics studies that have been published to date constitute a valuable and vast resource for biological discovery. While various \u2018atlas\u2019 projects have collated some of the associated datasets, most questions related to specific tissue types, species or other attributes of studies require identifying papers through manual and challenging literature search. To facilitate discovery with published single-cell transcriptomics data, we have assembled a near exhaustive, manually curated database of single-cell transcriptomics studies with key information: descriptions of the type of data and technologies used, along with descriptors of the biological systems studied. Additionally, the database contains summarized information about analysis in the papers, allowing for analysis of trends in the field. As an example, we show that the number of cell types identified in scRNA-seq studies is proportional to the number of cells analysed.<\/jats:p>\n                  <jats:p>Database URL: www.nxn.se\/single-cell-studies\/gui<\/jats:p>","DOI":"10.1093\/database\/baaa073","type":"journal-article","created":{"date-parts":[[2020,11,17]],"date-time":"2020-11-17T15:07:22Z","timestamp":1605625642000},"source":"Crossref","is-referenced-by-count":231,"title":["A curated database reveals trends in single-cell transcriptomics"],"prefix":"10.1093","volume":"2020","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9217-2330","authenticated-orcid":false,"given":"Valentine","family":"Svensson","sequence":"first","affiliation":[{"name":"Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eduardo","family":"da Veiga Beltrame","sequence":"additional","affiliation":[{"name":"Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[{"name":"Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA, 91125, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,11,28]]},"reference":[{"key":"2020112809064320700_R1","doi-asserted-by":"publisher","DOI":"10.1101\/104810","article-title":"scRNASeqDB: a database for gene expression profiling in human single cell by RNA-Seq","volume-title":"bioRxiv","author":"Cao","year":"2017"},{"key":"2020112809064320700_R2","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1038\/s41592-018-0175-z","article-title":"Spatial organization of the somatosensory cortex revealed by osmFISH","volume":"15","author":"Codeluppi","year":"2018","journal-title":"Nat. Methods"},{"key":"2020112809064320700_R3","doi-asserted-by":"publisher","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":"2020112809064320700_R4","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1101\/gr.110882.110","article-title":"Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq","volume":"21","author":"Islam","year":"2011","journal-title":"Genome Res."},{"key":"2020112809064320700_R5","doi-asserted-by":"publisher","DOI":"10.1242\/dev.181396","article-title":"Single cell analyses of development in the modern era","volume":"146","author":"Klein","year":"2019","journal-title":"Development"},{"key":"2020112809064320700_R6","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"2020112809064320700_R7","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nmeth.3370","article-title":"G&T-seq: parallel sequencing of single-cell genomes and transcriptomes","volume":"12","author":"Macaulay","year":"2015","journal-title":"Nat. Methods"},{"key":"2020112809064320700_R8","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"2020112809064320700_R9","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1093\/bioinformatics\/btg081","article-title":"Reconstructing the temporal ordering of biological samples using microarray data","volume":"19","author":"Magwene","year":"2003","journal-title":"Bioinformatics"},{"key":"2020112809064320700_R10","article-title":"UMAP: Uniform Manifold Approximation and Projection for dimension reduction","volume-title":"arXiv [stat.ML]. arXiv","author":"McInnes","year":"2018"},{"key":"2020112809064320700_R11","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":"2020112809064320700_R12","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.27041","article-title":"The Human Cell Atlas","volume":"6","author":"Regev","year":"2017","journal-title":"eLife"},{"key":"2020112809064320700_R13","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1016\/j.neuron.2016.10.001","article-title":"In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus","volume":"92","author":"Shah","year":"2016","journal-title":"Neuron"},{"key":"2020112809064320700_R14","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4612","article-title":"Bias, robustness and scalability in single-cell differential expression analysis","author":"Soneson","year":"2018","journal-title":"Nat. Methods"},{"key":"2020112809064320700_R15","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":"2020112809064320700_R16","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nprot.2017.149","article-title":"Exponential scaling of single-cell RNA-seq in the past decade","volume":"13","author":"Svensson","year":"2018","journal-title":"Nat. Protoc."},{"key":"2020112809064320700_R17","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2020112809064320700_R18","article-title":"Visualizing data using t-SNE","volume":"9","author":"Van der Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"2020112809064320700_R19","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat5691","article-title":"Three-dimensional intact-tissue sequencing of single-cell transcriptional states","volume":"361","author":"Wang","year":"2018","journal-title":"Science"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa073\/34568703\/baaa073.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa073\/34568703\/baaa073.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,28]],"date-time":"2020-11-28T09:06:52Z","timestamp":1606554412000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa073\/6008692"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"references-count":19,"URL":"https:\/\/doi.org\/10.1093\/database\/baaa073","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/742304","asserted-by":"object"}]},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020]]},"published":{"date-parts":[[2020]]},"article-number":"baaa073"}}