Correlation of myeloid-derived suppressor cell expansion with upregulated transposable elements in severe COVID-19 un-veiled in single-cell RNA sequencing reanalysis
Genome indexes were generated and Patients' paired-end FASTQ files were mapped to them.transposable element were quantified using scTE package algorithm.
Part II: Preprocessing, analysis, and exploration of scRNA-seq data
Defferential expression tables for each cluster in compares to other clusters
Dependencies
zellkonverter,SingleCellExperiment,Seurat
Summary
count matrixes were preprocessed(ig.,filtering,normalizaton).The bach effects between samples were removed and all-samples of each condition(ie,healthy,mild and severe conditions) were integrated.After scaling data, PCA was performed and The KNN graph was conducted based on the PCA-reduced data, and unsupervised clustering was performed.Differential expression analysis was conducted based on the 'MAST' method.
Average expression levels of gene-sets pathways in neutrophil clusters and upregulated genes in these clusters(logfc>0.7 and p.adj<0.05) were calculated and the correlation between these pathways and upregulated genes in neutrophil clusters was evaluated.