REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
See Data S1	(Bjornson-Hooper et al., 2019a, 2019b)	N/A
Bacterial and Virus Strains
Ebola virus/H. sapiens-tc/COD/1995/Kikwit-9510621 (EBOV/Kikwit; GenBank accession MG572235.1; Filoviridae: Zaire ebolavirus)	BEI Resources	Cat#NR-50306
Chemicals, Peptides, and Recombinant Proteins
Xpert Ebola Lysis Reagent	Cepheid	Cat#GXEBOLA-CE-50
EnGen SauCas9, 20 μM	(Yourik et al., 2019); NEB	Cat#M0654T
16% paraformaldehyde	Electron Microscopy Sciences	Cat#15710
Deposited Data
EBOV NHP infection single-cell RNA-Seq	This paper	GEO: GSE158390
EBOV NHP infection CyTOF	This paper	FlowRepository: FR-FCM-Z2LX
Human cell atlas bone marrow scRNA-Seq	(Hay et al., 2018)	https://data.humancellatlas.org/
Human healthy PBMC scRNA-Seq	10X	https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”
EBOV human infection CyTOF	(McElroy et al., 2020)	Author correspondence
Oligonucleotides
Primer: dN-SMRT: AAGCAGTGGTATCAACGCAG AGTGANNNGGNNNB	(Hughes et al., 2020); IDT	N/A
gRNA sequence: DASH_SeqB: GGGNNNNAAGC AGUGGUAUCAACGGUUAUAGUACUCUGGAAA CAGAAUCUACUAAAACAAGGCAAAAUGCCGUG UUUAUCUCGUCAACUUGUUGGCGAGAU	This paper	N/A
Software and Algorithms
DropSeqPipe	(Macosko et al., 2015)	https://github.com/Hoohm/dropSeqPipe
Scanpy	(Wolf et al., 2018)	https://github.com/theislab/scanpy
MAST	(Finak et al., 2015)	https://github.com/RGLab/MAST
HARMONY	(Korsunsky et al., 2019)	https://pypi.org/project/harmony-pytorch/, https://github.com/immunogenomics/harmony
MAGIC	(van Dijk et al., 2018)	https://github.com/KrishnaswamyLab/MAGIC
cNMF	(Kotliar et al., 2019)	https://github.com/dylkot/cNMF
Scrublet	(Wolock et al., 2019)	https://github.com/AllonKleinLab/scrublet