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

doi:10.1016/j.isci.2022.104318

hECA: The cell-centric assembly of a cell atlas

iScience. 2022 Apr 28;25(5):104318. doi: 10.1016/j.isci.2022.104318. eCollection 2022 May 20.

Authors

Sijie Chen¹, Yanting Luo¹, Haoxiang Gao¹, Fanhong Li¹, Yixin Chen¹, Jiaqi Li¹, Renke You², Minsheng Hao¹, Haiyang Bian¹, Xi Xi¹, Wenrui Li¹, Weiyu Li², Mingli Ye², Qiuchen Meng¹, Ziheng Zou¹, Chen Li¹, Haochen Li³, Yangyuan Zhang¹, Yanfei Cui¹, Lei Wei¹, Fufeng Chen², Xiaowo Wang¹, Hairong Lv^{1

2}, Kui Hua¹, Rui Jiang¹, Xuegong Zhang^{1

3

4}

Affiliations

¹ MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
² Fuzhou Institute of Data Technology, Changle, Fuzhou 350200, China.
³ School of Medicine, Tsinghua University, Beijing 100084, China.
⁴ School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.

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.

Keywords: Bioinformatics; Cell biology; Stem cells research.