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hECA: The cell-centric assembly of a cell atlas.
Chen, Sijie; Luo, Yanting; Gao, Haoxiang; Li, Fanhong; Chen, Yixin; Li, Jiaqi; You, Renke; Hao, Minsheng; Bian, Haiyang; Xi, Xi; Li, Wenrui; Li, Weiyu; Ye, Mingli; Meng, Qiuchen; Zou, Ziheng; Li, Chen; Li, Haochen; Zhang, Yangyuan; Cui, Yanfei; Wei, Lei; Chen, Fufeng; Wang, Xiaowo; Lv, Hairong; Hua, Kui; Jiang, Rui; Zhang, Xuegong.
Afiliação
  • Chen S; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Luo Y; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Gao H; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li F; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Chen Y; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li J; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • You R; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
  • Hao M; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Bian H; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Xi X; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li W; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li W; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
  • Ye M; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
  • Meng Q; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Zou Z; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li C; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Li H; School of Medicine, Tsinghua University, Beijing 100084, China.
  • Zhang Y; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Cui Y; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Wei L; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Chen F; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
  • Wang X; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Lv H; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Hua K; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
  • Jiang R; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
  • Zhang X; MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
iScience ; 25(5): 104318, 2022 May 20.
Article em En | MEDLINE | ID: mdl-35602947
ABSTRACT
The accumulation of massive single-cell omics data provides growing resources for building biomolecular atlases of all cells of human organs or the whole body. The true assembly of a cell atlas should be cell-centric rather than file-centric. We developed a unified informatics framework for seamless cell-centric data assembly and built the human Ensemble Cell Atlas (hECA) from scattered data. hECA v1.0 assembled 1,093,299 labeled human cells from 116 published datasets, covering 38 organs and 11 systems. We invented three new methods of atlas applications based on the cell-centric assembly "in data" cell sorting for targeted data retrieval with customizable logic expressions, "quantitative portraiture" for multi-view representations of biological entities, and customizable reference creation for generating references for automatic annotations. Case studies on agile construction of user-defined sub-atlases and "in data" investigation of CAR-T off-targets in multiple organs showed the great potential enabled by the cell-centric ensemble atlas.
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2022 Tipo de documento: Article
Texto completo
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XML
PubMed Links
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2022 Tipo de documento: Article