Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA

Yixin Chen; Minsheng Hao; Haoxiang Gao; Jiaqi Li; Sijie Chen; Fanhong Li; Lei Wei; Xuegong Zhang

doi:10.1016/j.xpro.2022.101589

Protocol for profiling cell-centric assembled single-cell human transcriptome data in hECA

STAR Protoc. 2022 Jul 31;3(3):101589. doi: 10.1016/j.xpro.2022.101589. eCollection 2022 Sep 16.

Authors

Yixin Chen¹, Minsheng Hao¹, Haoxiang Gao¹, Jiaqi Li¹, Sijie Chen¹, Fanhong Li¹, Lei Wei², Xuegong Zhang³

Affiliations

¹ MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China.
² MOE Key Lab of Bioinformatics, Bioinformatics Division of BNRIST and Department of Automation, Tsinghua University, Beijing 100084, China. Electronic address: weilei92@tsinghua.edu.cn.
³ 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. Electronic address: zhangxg@tsinghua.edu.cn.

Abstract

Human Ensemble Cell Atlas (hECA) provides a unified informatics framework and the cell-centric-assembled single-cell transcriptome data of 1,093,299 labeled human cells from 116 published datasets. In this protocol, we provide three applications of hECA: "quantitative portraiture" exploration with websites, customizable reference creation for automatic cell type annotation, and "in data" cell sorting with logical conditions. We provide detail steps of connecting to the database, searching cell with conditions, downloading data, and annotating new datasets with customized reference. For complete details on the use and execution of this protocol, please refer to Chen et al. (2022).

Keywords: Bioinformatics; Computer sciences; Gene Expression; RNAseq; Single Cell.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Neoplasm Proteins*
Transcriptome* / genetics

Substances

HECA protein, human
Neoplasm Proteins