SAVER: gene expression recovery for single-cell RNA sequencing
In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-c...
Gespeichert in:
| Veröffentlicht in: | Nature methods 2018-07, Vol.15 (7), p.539-542 |
|---|---|
| Hauptverfasser: | , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 542 |
|---|---|
| container_issue | 7 |
| container_start_page | 539 |
| container_title | Nature methods |
| container_volume | 15 |
| creator | Huang, Mo Wang, Jingshu Torre, Eduardo Dueck, Hannah Shaffer, Sydney Bonasio, Roberto Murray, John I. Raj, Arjun Li, Mingyao Zhang, Nancy R. |
| description | In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.
SAVER accurately recovers expression values in single-cell RNA-sequencing data to improve downstream analysis. |
| doi_str_mv | 10.1038/s41592-018-0033-z |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6030502</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2063687917</sourcerecordid><originalsourceid>FETCH-LOGICAL-c470t-cafa67c27a5753978733e1f1707e293d941a352983092cb36ac5643ce10b21ea3</originalsourceid><addsrcrecordid>eNp1kUlLAzEUx4MoLtUP4EUGvHgZzTKZTDwIpdQFRKEu15Cmb8aRaVKTtqif3gxdXMBTHnm_93_LH6FDgk8JZsVZyAiXNMWkSDFmLP3cQLuEZ0UqCOabqxhLsoP2QnhtmYzybbRDpcxIIdguunjoPvcH50kFFhJ4n3gIoXY28WDcHPxHUjqfhNpWDaQGmiYZ3HWTAG8zsCb-7qOtUjcBDpZvBz1d9h971-nt_dVNr3ubmkzgaWp0qXNhqNBccCZFbM2AlERgAVSyUZxGM05lwbCkZshybXieMQMEDykBzTroYqE7mQ3HMDJgp143auLrsfYfyula_c7Y-kVVbq5yzDDHNAqcLAW8i8OHqRrXoV1IW3CzoCjmkhcs3jOix3_QVzfzNq4XqZzlhZBERIosKONdCB7K9TAEq9YdtXBHRXdUe3n1GWuOfm6xrljZEQG6AEJM2Qr8d-v_Vb8AKayZlQ</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2063687917</pqid></control><display><type>article</type><title>SAVER: gene expression recovery for single-cell RNA sequencing</title><source>MEDLINE</source><source>Springer Nature - Complete Springer Journals</source><source>Nature Journals Online</source><creator>Huang, Mo ; Wang, Jingshu ; Torre, Eduardo ; Dueck, Hannah ; Shaffer, Sydney ; Bonasio, Roberto ; Murray, John I. ; Raj, Arjun ; Li, Mingyao ; Zhang, Nancy R.</creator><creatorcontrib>Huang, Mo ; Wang, Jingshu ; Torre, Eduardo ; Dueck, Hannah ; Shaffer, Sydney ; Bonasio, Roberto ; Murray, John I. ; Raj, Arjun ; Li, Mingyao ; Zhang, Nancy R.</creatorcontrib><description>In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.
SAVER accurately recovers expression values in single-cell RNA-sequencing data to improve downstream analysis.</description><identifier>ISSN: 1548-7091</identifier><identifier>EISSN: 1548-7105</identifier><identifier>DOI: 10.1038/s41592-018-0033-z</identifier><identifier>PMID: 29941873</identifier><language>eng</language><publisher>New York: Nature Publishing Group US</publisher><subject>631/114/2415 ; 631/114/794 ; 631/1647/2017 ; 631/1647/514/1949 ; Animals ; Base Sequence ; Bioinformatics ; Biological Microscopy ; Biological Techniques ; Biomedical and Life Sciences ; Biomedical Engineering/Biotechnology ; Brief Communication ; Cerebral Cortex - cytology ; Data recovery ; Gene expression ; Gene Expression Profiling - methods ; Gene sequencing ; Genes ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Life Sciences ; Mice ; Molecular chains ; Proteomics ; Ribonucleic acid ; RNA ; RNA - chemistry ; RNA - genetics ; Sequence Analysis, RNA - methods ; Single-Cell Analysis - methods ; Software</subject><ispartof>Nature methods, 2018-07, Vol.15 (7), p.539-542</ispartof><rights>The Author(s) 2018</rights><rights>Copyright Nature Publishing Group Jul 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c470t-cafa67c27a5753978733e1f1707e293d941a352983092cb36ac5643ce10b21ea3</citedby><cites>FETCH-LOGICAL-c470t-cafa67c27a5753978733e1f1707e293d941a352983092cb36ac5643ce10b21ea3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41592-018-0033-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41592-018-0033-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29941873$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Huang, Mo</creatorcontrib><creatorcontrib>Wang, Jingshu</creatorcontrib><creatorcontrib>Torre, Eduardo</creatorcontrib><creatorcontrib>Dueck, Hannah</creatorcontrib><creatorcontrib>Shaffer, Sydney</creatorcontrib><creatorcontrib>Bonasio, Roberto</creatorcontrib><creatorcontrib>Murray, John I.</creatorcontrib><creatorcontrib>Raj, Arjun</creatorcontrib><creatorcontrib>Li, Mingyao</creatorcontrib><creatorcontrib>Zhang, Nancy R.</creatorcontrib><title>SAVER: gene expression recovery for single-cell RNA sequencing</title><title>Nature methods</title><addtitle>Nat Methods</addtitle><addtitle>Nat Methods</addtitle><description>In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.
SAVER accurately recovers expression values in single-cell RNA-sequencing data to improve downstream analysis.</description><subject>631/114/2415</subject><subject>631/114/794</subject><subject>631/1647/2017</subject><subject>631/1647/514/1949</subject><subject>Animals</subject><subject>Base Sequence</subject><subject>Bioinformatics</subject><subject>Biological Microscopy</subject><subject>Biological Techniques</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedical Engineering/Biotechnology</subject><subject>Brief Communication</subject><subject>Cerebral Cortex - cytology</subject><subject>Data recovery</subject><subject>Gene expression</subject><subject>Gene Expression Profiling - methods</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>High-Throughput Nucleotide Sequencing - methods</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Mice</subject><subject>Molecular chains</subject><subject>Proteomics</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><subject>RNA - genetics</subject><subject>Sequence Analysis, RNA - methods</subject><subject>Single-Cell Analysis - methods</subject><subject>Software</subject><issn>1548-7091</issn><issn>1548-7105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNp1kUlLAzEUx4MoLtUP4EUGvHgZzTKZTDwIpdQFRKEu15Cmb8aRaVKTtqif3gxdXMBTHnm_93_LH6FDgk8JZsVZyAiXNMWkSDFmLP3cQLuEZ0UqCOabqxhLsoP2QnhtmYzybbRDpcxIIdguunjoPvcH50kFFhJ4n3gIoXY28WDcHPxHUjqfhNpWDaQGmiYZ3HWTAG8zsCb-7qOtUjcBDpZvBz1d9h971-nt_dVNr3ubmkzgaWp0qXNhqNBccCZFbM2AlERgAVSyUZxGM05lwbCkZshybXieMQMEDykBzTroYqE7mQ3HMDJgp143auLrsfYfyula_c7Y-kVVbq5yzDDHNAqcLAW8i8OHqRrXoV1IW3CzoCjmkhcs3jOix3_QVzfzNq4XqZzlhZBERIosKONdCB7K9TAEq9YdtXBHRXdUe3n1GWuOfm6xrljZEQG6AEJM2Qr8d-v_Vb8AKayZlQ</recordid><startdate>20180701</startdate><enddate>20180701</enddate><creator>Huang, Mo</creator><creator>Wang, Jingshu</creator><creator>Torre, Eduardo</creator><creator>Dueck, Hannah</creator><creator>Shaffer, Sydney</creator><creator>Bonasio, Roberto</creator><creator>Murray, John I.</creator><creator>Raj, Arjun</creator><creator>Li, Mingyao</creator><creator>Zhang, Nancy R.</creator><general>Nature Publishing Group US</general><general>Nature Publishing Group</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7QO</scope><scope>7SS</scope><scope>7TK</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PCBAR</scope><scope>PDBOC</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180701</creationdate><title>SAVER: gene expression recovery for single-cell RNA sequencing</title><author>Huang, Mo ; Wang, Jingshu ; Torre, Eduardo ; Dueck, Hannah ; Shaffer, Sydney ; Bonasio, Roberto ; Murray, John I. ; Raj, Arjun ; Li, Mingyao ; Zhang, Nancy R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c470t-cafa67c27a5753978733e1f1707e293d941a352983092cb36ac5643ce10b21ea3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>631/114/2415</topic><topic>631/114/794</topic><topic>631/1647/2017</topic><topic>631/1647/514/1949</topic><topic>Animals</topic><topic>Base Sequence</topic><topic>Bioinformatics</topic><topic>Biological Microscopy</topic><topic>Biological Techniques</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedical Engineering/Biotechnology</topic><topic>Brief Communication</topic><topic>Cerebral Cortex - cytology</topic><topic>Data recovery</topic><topic>Gene expression</topic><topic>Gene Expression Profiling - methods</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>High-Throughput Nucleotide Sequencing - methods</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Mice</topic><topic>Molecular chains</topic><topic>Proteomics</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><topic>RNA - genetics</topic><topic>Sequence Analysis, RNA - methods</topic><topic>Single-Cell Analysis - methods</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Huang, Mo</creatorcontrib><creatorcontrib>Wang, Jingshu</creatorcontrib><creatorcontrib>Torre, Eduardo</creatorcontrib><creatorcontrib>Dueck, Hannah</creatorcontrib><creatorcontrib>Shaffer, Sydney</creatorcontrib><creatorcontrib>Bonasio, Roberto</creatorcontrib><creatorcontrib>Murray, John I.</creatorcontrib><creatorcontrib>Raj, Arjun</creatorcontrib><creatorcontrib>Li, Mingyao</creatorcontrib><creatorcontrib>Zhang, Nancy R.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nature methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Huang, Mo</au><au>Wang, Jingshu</au><au>Torre, Eduardo</au><au>Dueck, Hannah</au><au>Shaffer, Sydney</au><au>Bonasio, Roberto</au><au>Murray, John I.</au><au>Raj, Arjun</au><au>Li, Mingyao</au><au>Zhang, Nancy R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SAVER: gene expression recovery for single-cell RNA sequencing</atitle><jtitle>Nature methods</jtitle><stitle>Nat Methods</stitle><addtitle>Nat Methods</addtitle><date>2018-07-01</date><risdate>2018</risdate><volume>15</volume><issue>7</issue><spage>539</spage><epage>542</epage><pages>539-542</pages><issn>1548-7091</issn><eissn>1548-7105</eissn><abstract>In single-cell RNA sequencing (scRNA-seq) studies, only a small fraction of the transcripts present in each cell are sequenced. This leads to unreliable quantification of genes with low or moderate expression, which hinders downstream analysis. To address this challenge, we developed SAVER (single-cell analysis via expression recovery), an expression recovery method for unique molecule index (UMI)-based scRNA-seq data that borrows information across genes and cells to provide accurate expression estimates for all genes.
SAVER accurately recovers expression values in single-cell RNA-sequencing data to improve downstream analysis.</abstract><cop>New York</cop><pub>Nature Publishing Group US</pub><pmid>29941873</pmid><doi>10.1038/s41592-018-0033-z</doi><tpages>4</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1548-7091 |
| ispartof | Nature methods, 2018-07, Vol.15 (7), p.539-542 |
| issn | 1548-7091 1548-7105 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_6030502 |
| source | MEDLINE; Springer Nature - Complete Springer Journals; Nature Journals Online |
| subjects | 631/114/2415 631/114/794 631/1647/2017 631/1647/514/1949 Animals Base Sequence Bioinformatics Biological Microscopy Biological Techniques Biomedical and Life Sciences Biomedical Engineering/Biotechnology Brief Communication Cerebral Cortex - cytology Data recovery Gene expression Gene Expression Profiling - methods Gene sequencing Genes High-Throughput Nucleotide Sequencing - methods Humans Life Sciences Mice Molecular chains Proteomics Ribonucleic acid RNA RNA - chemistry RNA - genetics Sequence Analysis, RNA - methods Single-Cell Analysis - methods Software |
| title | SAVER: gene expression recovery for single-cell RNA sequencing |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-13T17%3A37%3A27IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=SAVER:%20gene%20expression%20recovery%20for%20single-cell%20RNA%20sequencing&rft.jtitle=Nature%20methods&rft.au=Huang,%20Mo&rft.date=2018-07-01&rft.volume=15&rft.issue=7&rft.spage=539&rft.epage=542&rft.pages=539-542&rft.issn=1548-7091&rft.eissn=1548-7105&rft_id=info:doi/10.1038/s41592-018-0033-z&rft_dat=%3Cproquest_pubme%3E2063687917%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2063687917&rft_id=info:pmid/29941873&rfr_iscdi=true |