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A curated database reveals trends in single cell transcriptomics

Svensson, Valentine and da Veiga Beltrame, Eduardo and Pachter, Lior (2020) A curated database reveals trends in single cell transcriptomics. Database: The Journal of Biological Databases and Curation, 2020 . Art. No. baaa073. ISSN 1758-0463. PMCID PMC7698659. https://resolver.caltech.edu/CaltechAUTHORS:20190821-092511308

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Abstract

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 ‘atlas’ 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/database/baaa073DOIArticle
https://doi.org/10.1101/742304DOIDiscussion Paper
https://www.nxn.se/single-cell-studies/guiRelated ItemDatabase
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7698659/PubMed CentralArticle
ORCID:
AuthorORCID
Svensson, Valentine0000-0002-9217-2330
da Veiga Beltrame, Eduardo0000-0002-1529-9207
Pachter, Lior0000-0002-9164-6231
Additional Information:© The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 14 October 2019; Revision received: 10 July 2020; Editorial decision: 03 August 2020; Accepted: 16 November 2020; Published: 28 November 2020. We thank Carlos Talavera-López for helpful feedback on the manuscript. Cloud infrastructure was partially funded through the Google Cloud Platform research credits program. The work was partly funded by NIH U19MH114830.
Funders:
Funding AgencyGrant Number
Google Cloud PlatformUNSPECIFIED
NIHU19MH114830
PubMed Central ID:PMC7698659
Record Number:CaltechAUTHORS:20190821-092511308
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190821-092511308
Official Citation:Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter, A curated database reveals trends in single-cell transcriptomics, Database, Volume 2020, 2020, baaa073, https://doi.org/10.1093/database/baaa073
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:98067
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Aug 2019 18:46
Last Modified:04 Dec 2020 17:09

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