Profiling ACE2 expression in colon tissue of healthy adults and colorectal cancer patients by single-cell transcriptome analysis

Haoyan Chen; Baoqin Xuan; Yuqing Yan; Xiaoqiang Zhu; Chaoqin Shen; Gang Zhao; Linhua Ji; Danhua Xu; Hua Xiong; TaChung Yu; Xiaobo Li; Qiang Liu; Yingxuan Chen; Yun Cui; Jie Hong; Jing-Yuan Fang

The copyright holder for this preprint . https://doi.org/10.1101/2020.02. 15.20023457 doi: medRxiv preprint genome (GRCh38) using CellRanger toolkit (version 3.0.2, 10X Genomics). The unique molecular identifier (UMI) count matrix was converted to anndata objects (version 0.6.22) using the Scanpy package v1.4.4 (pmid: 29409532). We utilized the following procedure to control for data quality: cells with fewer than 200 genes, and genes that are detected in less than 3 cells. Following the quality control procedure, the dataset consisted of 21,686 cells expressing 22,760 genes. The filtered gene expression matrix was normalized using Scanpy's sc.pp.normalize_total function. A single-cell neighborhood graph was computed on the 50 first principal components that sufficiently explain the variation in the data using 15 nearest neighbors. Uniform Manifold Approximation and Projection (UMAP) was run for visualization. Cell types were annotated based on the expression of known marker genes.