REAGENT or RESOURCE SOURCE IDENTIFIER
Biological Samples
M. mulatta lung, bone marrow, brain, colon, ileum, jejunum, liver, lung, peripheral blood, spleen, thymus, tonsil, and lymph nodes from various sites Washington National Primate Research Center N/A
Human lung tissue from surgical excess University of KwaZulu-Natal IRB Code:BE024/09
Human non-inflamed ileal pinch biopsies Multi-center clinical study, approved by the Institutional Review Board at Boston Children’s Hospital IRB Code:IRB-P00030890
Human nasal lavage University of Massachusetts Medical School N/A
Human nasal scraping, polyp scrapings, ethmoid sinus surgical tissue samples Partners HealthCare Institute N/A
M. fascicularis lung and granulomatous tissue University of Pittsburgh School of Medicine N/A
Antibodies
anti-ACE2 human antibody, goat polyclonal R&D Cat#AF933
Bacterial and Virus Strains
MHV-68 Adler et al., 2000 N/A
Mycobacterium Tuberculosis, Modified Erdman Strain Martin et al., 2017 N/A
Chemicals, Peptides, and Recombinant Proteins
2-Mercaptoethanol Sigma Cat#M3148-25ML
RLT Buffer QIAGEN Cat#79216
dNTP New England BioLabs Cat#N0447L
RNase Inhibitor Fisher Scientific Cat#AM2696
Maxima RNaseH-minus RT Enzyme Fisher Scientific Cat#EP0753
MgCl2 Sigma Cat#63069-100ML
Betaine Sigma Cat#B0300-5VL
AMPure RNAClean XP RNA-SPRI beads Beckman Coulter Cat#A63987
AMPure XP SPRI beads Beckman Coulter Cat#A63881
Guanidinium thiocyanate Sigma Cat#AM9422
Sarkosyl Sigma Cat#L7414
Exonuclease I New England BioLabs Cat#M0293S
Klenow Fragment New England BioLabs Cat#M0212L
DNase I Roche Cat#10104159001
Collagenase IV Life Technologies Cat#17104019
Collagenase D Roche Cat#11088858001
Liberase TM Roche Cat#5401119001
TrypLE Thermo Fisher Cat#12604013
ACK Buffer Thermo Fisher Cat#A1049201
IFN-α Biolegend Cat#752802
Dispase II Thermo Fisher Cat#17105041
Elastase Worthington Biochem Cat#LS002292
Pneumacult-Ex serum-free media StemCell Technologies, Inc. Cat#05040
IL-4, human Biolegend Cat#574002
IL17A, human Biolegend Cat#570502
IFNγ, human Biolegend Cat#570202
IFNγ, mouse Peprotech Cat#315-05
IFNα, human Biolegend Cat#592702
IFNα, mouse Biolegend Cat#752802
IFNβ, mouse R&D Systems Cat#8234-MB-010
Critical Commercial Assays
Nextera XT DNA Library Preparation Kit Illumina Cat#FC-131-1096
High Sensitivity D5000 ScreenTape Agilent Cat#5067-5592
Qubit dsDNA High-Sensitivity kit ThermoFisher Cat#Q32854
NextSeq 500/550 High Output v2 (75 cycles) Illumina Cat#FC-404-2005
NovaSeq 6000 S2 (100 cycles) Illumina Cat#20012862
Kapa HiFi HotStart ReadyMix Kapa Biosystems Cat#KK2602
MACOSKO-2011-10 mRNA Capture Beads ChemGenes Cat#NC0927472
Tumor Dissociation Kit, Human Miltenyi Biotec Cat#130-095-929
Chromium Single Cell 3′ v2 10X Genomics Cat#120237
Deposited Data
scRNA-seq Processed Data This paper https://singlecell.broadinstitute.org/single_cell?scpbr=the-alexandria-project
scRNA-seq Processed Data This paper https://drive.google.com/drive/folders/1bxCIqNeZ7wLuVOT16gphwj98_cc9KhrV?usp=sharing
scRNA-seq Processed Data This paper https://chanzuckerberg.github.io/cellxgene/posts/cellxgene_cziscience_com
scRNA-seq Processed Data This paper https://singlecell.broadinstitute.org/single_cell/covid19
scRNA-seq Processed Data (all species) and FASTQ files (for NHP and murine datasets) This paper GEO: GSE148829
scRNA-seq data from human nasal mucosa Ordovas-Montanes et al., 2018 https://singlecell.broadinstitute.org/single_cell/study/SCP253/allergic-inflammatory-memory-in-human-respiratory-epithelial-progenitor-cells
Human reference genome NCBI build 38 (GRCh38) Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Human reference genome NCBI build 19 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Mouse reference genome NCBI build 10 Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
Macaca mulatta reference genome assembly 8.0.1, annotation 102 NCBI Eukaryotic Genome Annotation Pipeline https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Macaca_mulatta/102/
Macaca fascicularis reference genome assembly 5, annotation 101 NCBI Eukaryotic Genome Annotation Pipeline https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Macaca_fascicularis/101/
Interferome Database Rusinova et al., 2013 http://www.interferome.org/
RNA-seq from human lung explants ± ex vivo IAV infection Matos et al., 2019 GEO: GSE135069
RNA-seq from human nasal epithelial cells Giovannini-Chami et al., 2012 GEO: GSE19190, GSE22147
Experimental Models: Cell Lines
Human: Passage 4 BEAS-2B ATCC CRL-9609
Experimental Models: Organisms/Strains
Mouse: C57BL/6J The Jackson Laboratory Cat#000664
Mouse: C57BL/6, IFNγR−/− B6.129S7-Ifngr1tm1Agt/J The Jackson Laboratory Cat#003288
Oligonucleotides
SMART-seq2 2 3′ Oligo-dT Primer: /5Biosg/AAG CAG TGG TAT CAA CGC AGA GTA CTT TTT TTT TTT TTT TTT TTT TTT TTT TTT TVN Integrated DNA Technologies N/A
SMART-seq2 5′ TSO: AAG CAG TGG TAT CAA CGC AGA GTA CAT rGrGrG Integrated DNA Technologies N/A
SMART-seq2 and Seq-Well ISPCR:AAG CAG TGG TAT CAA CGC AGA GT Integrated DNA Technologies N/A
Custom Read 1 Primer: GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C Integrated DNA Technologies N/A
Seq-Well 5′ TSO: AAG CAG TGG TAT CAA CGC AGA GTG AAT rGrGrG Integrated DNA Technologies N/A
Seq-Well Custom P5-SMART PCR hybrid oligo: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG CCT GTC CGC GGA AGC AGT GGT ATC AAC GCA GAG TAC Integrated DNA Technologies N/A
Seq-Well dN-SMRT oligo: AAG CAG TGG TAT CAA CGC AGA GTG ANN NGG NNN B Integrated DNA Technologies N/A
Software and Algorithms
R R Core Team https://www.r-project.org
R package – Seurat v2.3.4 and v3.1.0 Github https://github.com/satijalab/seurat
Scanpy Wolf et al., 2018 https://github.com/theislab/scanpy
R package – SCDE Bioconductor http://bioconductor.org/packages/scde/
Prism 6 GraphPad Software https://www.graphpad.com/scientific-software/prism/
STAR Github https://github.com/alexdobin/STAR
Uniform Manifold Approximation and Projection Github https://github.com/lmcinnes/umap
Rtsne CRAN https://cran.r-project.org/web/packages/Rtsne/