REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Immune Cell Profiling Panel (Core)	Nanostring Technologies, Inc	GMX-PROCONCT-HICP-12, Item 121300101, Lot# 0474026
10 Drug Target Panel	Nanostring Technologies, Inc	GMX-PROMODNCT-HIODT-12, Item 121300102, Lot# 0474029
Immune Activation Status Panel	Nanostring Technologies, Inc.	GMX-PROMODNCT-HIAS-12, Item 121300103, Lot# 0474032
Immune Cell Typing Panel	Nanostring Technologies, Inc	GMX-PROMODNCT-HICT-12, Item 121300104, Lot# 0474035
Cell Death Panel	Nanostring Technologies, Inc	GMX-PROMOD-NCTHCD-12, Lot# 0474050
MAPK Signaling Panel	Nanostring Technologies, Inc	GMX-PROMOD-NCTHMAPK-12, Lot# 0474047
Pl3K/AKT Signaling Panel	Nanostring Technologies, Inc	GMX-PROMOD-NCTHPl3K-12, Lot# 0474053
COVID-19 GeoMx-formatted Antibody Panel including (TMPRSS2, clone EPR3861; ACE2, clone EPR4436; Cathepsin L/V/K/H, clone EPR8011; DDX5, clone EPR7239; and SARS-CoV-2 spike glycoprotein, polyclonal)	Abcam	ab273594, Lot# GR3347471-1
GeoMx Solid Tumor TME Morphology Kit	Nanostring Technologies, Inc	GMX-PRO-MORPH-HST-12; Item 121300310
Alexa Fluor® 647 alpha-Smooth Muscle Actin Antibody, clone 1A4	Novus Bio	IC1420R
Biological samples
Autopsy tissues	Weill Cornell Medicine Department of Pathology	https://pathology.weill.cornell.edu/
Chemicals, peptides, and recombinant proteins
TRIzol	Invitrogen	Cat. #15596026
10% neutral buffered Formalin	Electron Microscopy Sciences	Cat. #15712
DNAse I	Zymo Research	Cat. #E1010
Critical commercial assays
Super-Script III Platinum SYBR Green One-Step qRT-PCR Kit	Invitrogen	Cat. #12594025
BD Univeral Viral Transport Media System	Becton, Dickinson and Company	Cat. #220526
QIAsymphony DSP Virus/Pathogen Mini Kit	Qiagen	Cat. #937036
NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads	New England BioLabs	Cat. #E7405
NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina	New England BioLabs	Cat. #E7760
TapeStation 2200	Agilent Technologies	Cat. #G2964AA
Kapa Biosystems Illumina library quantification kit	Roche	Cat. 07960140001
GeoMx DSP system	Nanostring Technologies, Inc	MAN-10088-03
Deposited data
Raw and analyzed RNA-seq data	This paper	dbGAP: accession #38851 and ID phs002258.v1.p1
Analyzed Nanostring GeoMx data	This paper	GEO: GSE169504
Human reference genome NCBI build 38, Gencode Human Release 33 (GRCH38.p13)	Genome Reference Consortium	http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Raw RNA-seq data	Rother et al.44	GSE159678
Reference scRNA-seq data	Travaglini et al.45; MacParland et al.46; Stewart et al.47; Wang et al.8	https://www.humancellatlas.org/
Molecular Signatures for GSEA (MSigDB)	Liberzon et al.48; Subramanian et al.49; Kuleshov et al.50; Sergushichev et al., 2016	http://www.gsea-msigdb.org/gsea/
Oligonucleotides
Primers for RT-PCR; ACTB-Forward: CGTCACCAACTGGGACGACA	This paper	N/A
Primers for RT-PCR; ACTB-Reverse: CTTCTCGCGGTTGGCCTTGG	This paper	N/A
Primers for RT-PCR; SARS-CoV-2-TRS-L: CTCTTGTAGATCTGTTCTCTAAACGAAC	This paper	N/A
Primers for RT-PCR; SARS-CoV-2-TRS-N: GGTCCACCAAACGTAATGCG	This paper	N/A
Software and algorithms
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
nf-core/rnaseq pipeline	Ewels et al.51	https://nf-co.re/rnaseq
FastQC	Andrews52	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Trim Galore!	N/A	https://github.com/FelixKrueger/TrimGalore
STAR	Dobin et al.53	https://github.com/alexdobin/STAR
Salmon	Patro et al.54	https://salmon.readthedocs.io/en/latest/salmon.html
Picard	N/A	https://github.com/broadinstitute/picard
StringTie	Kovaka et al.55	https://ccb.jhu.edu/software/stringtie/
Samtools	Li and Durbin56	http://samtools.sourceforge.net/
DESeq2 R package	Love et al.57	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
MuSiC R package	Wang et al.58	https://xuranw.github.io/MuSiC/articles/MuSiC.html
quanTIseq R package	Finotello et al.59	https://icbi.i-med.ac.at/software/quantiseq/doc/
Cocor R package	Diedenhofen and Musch60	https://cran.r-project.org/web/packages/cocor/cocor.pdf
synRNASeqNet R package	Luciano Garofano	https://github.com/cran/synRNASeqNet
Other
Resource page to visualize and explore autopsy RNA-seq data	This paper	https://covidgenes.weill.cornell.edu