iScience (May 2022)
hECA: The cell-centric assembly of a cell atlas
- Sijie Chen,
- Yanting Luo,
- Haoxiang Gao,
- Fanhong Li,
- Yixin Chen,
- Jiaqi Li,
- Renke You,
- Minsheng Hao,
- Haiyang Bian,
- Xi Xi,
- Wenrui Li,
- Weiyu Li,
- Mingli Ye,
- Qiuchen Meng,
- Ziheng Zou,
- Chen Li,
- Haochen Li,
- Yangyuan Zhang,
- Yanfei Cui,
- Lei Wei,
- Fufeng Chen,
- Xiaowo Wang,
- Hairong Lv,
- Kui Hua,
- Rui Jiang,
- Xuegong Zhang
Affiliations
- Sijie Chen
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Yanting Luo
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Haoxiang Gao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Fanhong Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Yixin Chen
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Jiaqi Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Renke You
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
- Minsheng Hao
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Haiyang Bian
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Xi Xi
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Wenrui Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Weiyu Li
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
- Mingli Ye
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
- Qiuchen Meng
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Ziheng Zou
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Chen Li
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Haochen Li
- School of Medicine, Tsinghua University, Beijing 100084, China
- Yangyuan Zhang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Yanfei Cui
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Lei Wei
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Fufeng Chen
- Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
- Xiaowo Wang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Hairong Lv
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China; Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China
- Kui Hua
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Rui Jiang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China
- Xuegong Zhang
- MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China; School of Medicine, Tsinghua University, Beijing 100084, China; School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; Corresponding author
- Journal volume & issue
-
Vol. 25,
no. 5
p. 104318
Abstract
Summary: 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.
