REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Aquaporin 4, C-terminus antibody	Millipore	Cat#AB3594; RRID: AB_91530
Anti-CD31 antibody	Abcam	Cat#ab28364; RRID: AB_726362
GFAP antibody	Novus Biologicals	Cat#NB300-141; RRID: AB_10001722
Cytokeratin 8 antibody	Novus Biologicals	Cat#NBP2-67468; RRID: AB_2922444
Mouse monoclonal MUC5AC antibody (45M1)	Thermo Fisher Scientific	Cat#MA5-12178; RRID: AB_10978001
Rabbit monoclonal SARS-CoV/SARS-CoV-2 Nucleocapsid antibody (clone #001)	Sino Biological	Cat#40143-R001; RRID: AB_2827974
Goat Anti-Olfactory Marker Protein Antibody, unconjugated	FUJIFILM Wako Shibayagi	Cat#544-10001-WAKO; RRID: AB_664696
Monoclonal Anti-Nerve Growth Factor Receptor (NGFR p75) antibody	Sigma-Aldrich	Cat#N5408; RRID: AB_477280
S100B Recombinant monoclonal antibody (S100B/1706R)	Enzo Life Sciences	Cat#ENZ-ABS307; RRID: AB_2922445
Rabbit polyclonal antiserum Somatostatin receptor subtype 2A	Biotrend	Cat#NB-49-016-50ul
ZO-1 tight junction protein antibody	Novus Biologicals	Cat#NBP1-85046; RRID: AB_11006040
Mouse monoclonal anti-Tubulin beta 3/TUBB3 (TUJ1)	BioLegend	Cat#801202; RRID: AB_10063408
Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488	Thermo Fisher Scientific	Cat#A32790; RRID: AB_2762833
Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 555	Thermo Fisher Scientific	Cat#A32794; RRID: AB_2762834
Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 555	Thermo Fisher Scientific	Cat#A32773; RRID: AB_2762848
Donkey anti-Goat IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 555	Thermo Fisher Scientific	Cat#A32816; RRID: AB_2762839
Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647	Thermo Fisher Scientific	Cat#A32795; RRID: AB_2762835
Donkey anti-Mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647	Thermo Fisher Scientific	Cat#A32787; RRID: AB_2762830
Donkey anti-Goat IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647	Thermo Fisher Scientific	Cat#A32849; RRID: AB_2762840
Biological samples
Tissue, blood, and CSF samples from COVID-19 patients and control patients	Ethical Committee of the University Hospitals Leuven, in Leuven, Belgium (S64042), the General Hospital Sint-Jan Brugge-Oostende AV in Bruges, Belgium (2736), and the Universitair Ziekenhuis Brussel in Brussels, Belgium (EC-2021-360)	clinicaltrials.gov (NCT04445597)
Chemicals, peptides, and recombinant proteins
Mount Solid antifade	abberior	Cat#MM-2011-2X15ML
RNAscope Target Retrieval Reagent	Advanced Cell Diagnostics	Cat#322000
RNAscope Protease III	Advanced Cell Diagnostics	Cat#322337
RNAscope Hydrogen Peroxide and Protease Plus	Advanced Cell Diagnostics	Cat# 322330
RNAscope Probe Diluent	Advanced Cell Diagnostics	Cat#300041
10% neutral buffered formalin	Electron Microscopy Sciences	Cat#15740-04
Tissue-Tek O.C.T. compound	Sakura	Cat#4583
Opal 520	Akoya Biosciences	Cat#FP1487001KT
Opal 570	Akoya Biosciences	Cat#FP1488001KT
Opal 690	Akoya Biosciences	Cat#FP1497001KT
1x Plus Amplification Diluents	Akoya Biosciences	Cat#FP1498
Donkey serum	Sigma-Aldrich	Cat#S30-100ML
Sucrose	Sigma-Aldrich	Cat#S0389-1KG
DAPI (4′,6-Diamidino-2-Phenylindole, Dihydrochloride)	Thermo Fisher Scientific	Cat#D1306
Critical commercial assays
RNAscope Multiplex Fluorescent Detection Kit v2	Advanced Cell Diagnostics	Cat#323110
RNAscope 4-Plex Ancillary Kit	Advanced Cell Diagnostics	Cat#323120
RNAscope Hs-FOXJ1 (C1)	Advanced Cell Diagnostics	Cat#430921
RNAscope Hs-FOXJ1 (C2)	Advanced Cell Diagnostics	Cat#430921-C2
RNAscope Hs-OMP (C1)	Advanced Cell Diagnostics	Cat#824181
RNAscope Hs-PECAM1-O1 (C1)	Advanced Cell Diagnostics	Cat#487381-C1
RNAscope Hs-PECAM1-O1 (C2)	Advanced Cell Diagnostics	Cat#487381-C2
RNAscope Hs-PECAM1-O1 (C4)	Advanced Cell Diagnostics	Cat#487381-C4
RNAscope Hs-UGT2A1 (C1)	Advanced Cell Diagnostics	Cat#814271
RNAscope V-nCoV-N (C1)	Advanced Cell Diagnostics	Cat#846081
RNAscope V-nCoV-N (C2)	Advanced Cell Diagnostics	Cat#846081-C2
RNAscope V-SARS-CoV-2-N-O2-sense (C1)	Advanced Cell Diagnostics	Cat#863841
RNAscope V-SARS-CoV-2-N-O2-sense (C3)	Advanced Cell Diagnostics	Cat#863841-C3
RNAscope V-nCoV2019-orf1ab-sense (C1)	Advanced Cell Diagnostics	Cat#859151
RNAscope V-nCoV2019-S (C1)	Advanced Cell Diagnostics	Cat#848561
RNAscope V-nCoV2019-S-sense (C1)	Advanced Cell Diagnostics	Cat#845701
RNAscope V-nCoV2019-S-sense (C3)	Advanced Cell Diagnostics	Cat#845701-C3
RNAscope V-nCoV-orf1ab-O1 (C1)	Advanced Cell Diagnostics	Cat#859981
Software and algorithms
Zeiss ZEN 2.6 system	Zeiss	https://www.zeiss.com
GraphPad Prism v9.2	GraphPad	https://graphpad.com
Adobe Illustrator 2020	Adobe	Adobe Creative Cloud
Adobe Acrobat Pro DC	Adobe	Adobe Creative Cloud
Other
Zeiss LSM 800	Zeiss	https://www.zeiss.com
Leica CM3050 S cryostat	Leica	https://www.leicabiosystems.com