{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T08:02:56Z","timestamp":1789718576319,"version":"4.0.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Zhengzhou Tobacco Research Institute","award":["110202401003(JY-03)"],"award-info":[{"award-number":["110202401003(JY-03)"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Zhengzhou Tobacco Research Institute","award":["902023CK0890"],"award-info":[{"award-number":["902023CK0890"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Zhengzhou Tobacco Research Institute","award":["110202201001(JY-01)"],"award-info":[{"award-number":["110202201001(JY-01)"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Zhengzhou Tobacco Research Institute","award":["2023000CC0110"],"award-info":[{"award-number":["2023000CC0110"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Zhengzhou Tobacco Research Institute","award":["2024900CC0270"],"award-info":[{"award-number":["2024900CC0270"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Zhengzhou Tobacco Research Institute","award":["2024200CC0130"],"award-info":[{"award-number":["2024200CC0130"]}],"id":[{"id":"https:\/\/ror.org\/0099xbw16","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The rapid advancement of single-cell technologies has significantly enhanced our ability to investigate cellular heterogeneity within plant tissues. However, deciphering these intricate cellular landscapes requires processing high-dimensional gene expression matrices and integrating diverse datasets to enable accurate marker selection, cell identification, and other complex computational operations. These processes typically require broad programming expertise, posing a challenge for researchers with a limited computational background. To address this, we present integrated Plant single-cell Database (iPscDB), an integrated and multifunctional platform that facilitates the integration and analysis of plant single-cell data. iPscDB combines 4\u2009688\u2009428 cells and 288\u2009139 curated cell markers derived from 946 experiments across 38 plant species. Wherever raw data were available, datasets were reprocessed through a single uniform pipeline, and both integration quality and automated cell-type annotation were benchmarked quantitatively. The platform introduces a Marker Confidence Level scheme that grades each cell-type marker by the strength and independence of its supporting evidence (from manually curated classic markers to database-derived associations), allowing users to judge marker reliability directly. The platform also provides a user-friendly online analysis pipeline and modules capable of processing raw FASTQ files or Cell Ranger-processed files. Users can configure parameters via an intuitive interface and utilize an integrated image editor to customize visualization outputs. Additionally, iPscDB supports various analyses, including cross-species gene expression, electronic Single-Cell Pictograph, and developmental trajectory. By streamlining the complex workflows of single-cell transcriptomics, iPscDB offers a practical and accessible resource for researchers with diverse technical backgrounds. iPscDB is accessible at\u00a0https:\/\/www.tobaccodb.org\/ipscdb\/homePage.<\/jats:p>","DOI":"10.1093\/nar\/gkag909","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T11:20:21Z","timestamp":1788780021000},"source":"Crossref","is-referenced-by-count":0,"title":["iPscDB: a comprehensive platform for plant single-cell transcriptomic data integration and analysis"],"prefix":"10.1093","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9898-3951","authenticated-orcid":false,"given":"Peng","family":"Lu","sequence":"first","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]},{"name":"Beijing Life Science Academy , Beijing 102200 ,","place":["China"]},{"name":"School of Software Technology, Zhejiang 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,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linggai","family":"Cao","sequence":"additional","affiliation":[{"name":"Guizhou Academy of Tobacco Science , Guiyang 550081 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2162-3819","authenticated-orcid":false,"given":"Shizhou","family":"Yu","sequence":"additional","affiliation":[{"name":"Guizhou Academy of Tobacco Science , Guiyang 550081 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sujie","family":"Wang","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-9540-7168","authenticated-orcid":false,"given":"Huan","family":"Su","sequence":"additional","affiliation":[{"name":"China Tobacco 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Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-2405-1414","authenticated-orcid":false,"given":"Jianfeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Life Science Academy , Beijing 102200 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yalong","family":"Xu","sequence":"additional","affiliation":[{"name":"China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC , Zhengzhou 450001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangyang","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Software Technology, Zhejiang University , Ningbo 315048 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