PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data
Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to...
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| Published in | Database : the journal of biological databases and curation Vol. 2019 |
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| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
2019
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to access for biological researchers due to the need for data processing using complex computational pipelines. We have implemented an online database, PanglaoDB, accessible through a user-friendly interface that can be used to explore published mouse and human single cell RNA sequencing studies. PanglaoDB contains pre-processed and pre-computed analyses from more than 1054 single-cell experiments covering most major single cell platforms and protocols, based on more than 4 million cells from a wide range of tissues and organs. The online interface allows users to query and explore cell types, genetic pathways and regulatory networks. In addition, we have established a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types. |
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| AbstractList | Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds of single-cell sequencing datasets have already been published. However, studies are frequently deposited as raw data, a format difficult to access for biological researchers due to the need for data processing using complex computational pipelines. We have implemented an online database, PanglaoDB, accessible through a user-friendly interface that can be used to explore published mouse and human single cell RNA sequencing studies. PanglaoDB contains pre-processed and pre-computed analyses from more than 1054 single-cell experiments covering most major single cell platforms and protocols, based on more than 4 million cells from a wide range of tissues and organs. The online interface allows users to query and explore cell types, genetic pathways and regulatory networks. In addition, we have established a community-curated cell-type marker compendium, containing more than 6000 gene-cell-type associations, as a resource for automatic annotation of cell types. |
| Author | Gan, Li-Ming Björkegren, Johan L M Franzén, Oscar |
| AuthorAffiliation | 1 Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden 2 Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, Mölndal, Sweden 3 Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA |
| AuthorAffiliation_xml | – name: 2 Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, Mölndal, Sweden – name: 1 Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden – name: 3 Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA |
| Author_xml | – sequence: 1 givenname: Oscar surname: Franzén fullname: Franzén, Oscar organization: Integrated Cardio Metabolic Centre (ICMC), Department of Medicine, Karolinska Institutet, Novum SE Huddinge, Sweden – sequence: 2 givenname: Li-Ming surname: Gan fullname: Gan, Li-Ming organization: Cardiovascular, Renal and Metabolism Translational Medicines Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Pepparedsleden, Mölndal, Sweden – sequence: 3 givenname: Johan L M surname: Björkegren fullname: Björkegren, Johan L M organization: Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30951143$$D View this record in MEDLINE/PubMed http://kipublications.ki.se/Default.aspx?queryparsed=id:141080532$$DView record from Swedish Publication Index |
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