The journal link: PLOS journal link

The alignment is done in a hybrid manner with human+SARS-CoV-2 viral genome reference (Homo_sapiens.GRCh38; MN985325)

The hybrid genome bash script: hybrid_pipeline_bash_script.sh

The raw data can be found in NCBI GEO website: GSE157526

This NCBI GEO website includes raw count matrix for each experimental data set.

• Concatenating nucleotide and assembly's annotation and gtf files
• Creating Cell Ranger reference
• Alignment and Count using Cell Ranger Count for each of the sample (the filter criteria for empty droplets are minimum 1000 genes per cell)

The Seurat hybrid pipeline: hybrid_pipeline_seurat_R_script.R

The CoV2 cells analysis (an extension from the Seurat hybrid pipeline: CoV2_cells_analysis_seurat_R_script.R

• QC and filtering on metadata (filter for genes with minimum three cells and for mitochondria genes percentage less than 30%)
• Data normalization, scaling, and detection of variable genes
• Dimensionality Reduction using PCA and clustering analysis (mitochondria and viral genes excluded)
• Find all gene markers and key genes results visualization

• Subset data for lower threshold of 0.0000001, 0.000001, 0.00001, 0.0001, 0.001, 0.01, 0.1% CoV2 cells
• Plot TSNE dimensionality reduction with specific threshold virus cells highlighted

The Seurat integration pipeline: integration_pipeline_seurat_v3_R_script.R

This pipeline includes CoV2 (definition >0.001% CoV2) and IFN cell analysis.

• Update Seurat object to v3
• Merge and integrate anchorset
• Normalization and scalling
• Dimensionality reduction: PCA and UMAP resolution 0.15
• Plot UMAP cell highlight for CoV2 (>0.001% cadetblue color) and IFN (red color)
• Plot FeatureScatter normalized CoV2 and IFN for sample 2 (24h) and 5 (48h)