Selected article for: "downstream analysis and gene expression"
Author: Lulin Zhou; Zubiao Niu; Xiaoyi Jiang; Zhengrong Zhang; You Zheng; Zhongyi Wang; Yichao Zhu; Lihua Gao; Xiaoning Wang; Qiang Sun
Title: Systemic analysis of tissue cells potentially vulnerable to SARS-CoV-2 infection by the protein-proofed single-cell RNA profiling of ACE2, TMPRSS2 and Furin proteases
  • Document date: 2020_4_10
    • ID: 3btc31kj_9
    Snippet: The raw count matrices were imported into R (version3.6.1, https://www.r-project.org/) and processed by the Seurat R package(version3.1.4) [38] . The filter criteria of low-quality cells were determined on the basis of the number of genes and the percentage of mitochondrial genes in the distinct tissue samples. Generally, cells with less than 200 detected genes, higher than 2500 detected genes and higher than 25% mitochondrial genome transcript r.....
    Document: The raw count matrices were imported into R (version3.6.1, https://www.r-project.org/) and processed by the Seurat R package(version3.1.4) [38] . The filter criteria of low-quality cells were determined on the basis of the number of genes and the percentage of mitochondrial genes in the distinct tissue samples. Generally, cells with less than 200 detected genes, higher than 2500 detected genes and higher than 25% mitochondrial genome transcript ratio were removed. Specially, cells with higher than 72% mitochondrial genome transcript ratio in the heart dataset and cells with higher than 50% mitochondrial genome transcript ratio in the liver dataset were removed as mentioned by the corresponding authors [27, 34] . Then, the gene expression matrices were normalized and scaled. Briefly, for each cell, the expression counts for each gene were divided by the sum of counts for all genes of that cell, multiplied by a scaling factor (10, 000) and log transformed using the "Normalize Data" function in the R package Seurat. Furthermore, 2000 highly variable genes were selected based on a variance stabilizing transformation method for downstream analysis.

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