Single cell transcriptome reveals aberrant macrophage subtype and its regulatory genes in critical COVID-19 patients

allGOnKEGG_June2020.gmt: Tab delimited file describing gene sets from KEGG and GO pathways

Control1_Deprez_exprMatrix.tsv: COntrol dataset 1

Contro2_Madissoon_lung.cellxgene.h5ad: Control dataset 2

COVID19COMORBID_DATABASE_UDDINLAB.xls: Comorbid gene dataset. The genes which are upregulated in severe COVID19-comorbid conditions

Final_LUNGMarker_DB_UDDINLAB.xlsx: Database consisting of canonical markers for cells associated to human lung region constructed by combining cell marker databases and thorough literature

All files starting with GSM: Matrix(h5 file) and annotation file for bronchoalveolar lavage fluid (BALF) from 6 severe and 3 moderate COVID-19 patients and 3 healthy control (From Liao et al., 2020: PMID: 32398875)

Human_cell_markers.txt: Markers from CellMarker database

PanglaoDB_markers_27_Mar_2020.tsv: Markers from PanglaoDB database

All files starting with sample: Sample Seurat processed file (sample.rds); Sample file for executing gene enrichment analysis; Sample file for lung marker database

All files starting with Validation: Validation files used in the paper.