REAGENT or RESOURCE	SOURCE	IDENTIFIER
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
Biological samples
Monkey Adrenal Total RNA, Rhesus	Zyagen	UR-501
Monkey Brain Total RNA, Rhesus	Zyagen	UR-201
Monkey Kidney Total RNA, Rhesus	Zyagen	UR-901
Monkey Liver Total RNA, Rhesus	Zyagen	UR-314
Monkey Lymph nodes Total RNA, Rhesus	Zyagen	UR-703
Monkey Skin Total RNA Total RNA, Rhesus	Zyagen	UR-101
Monkey Spinal cord Total RNA, Rhesus	Zyagen	UR-230
Monkey Spleen Total RNA, Rhesus	Zyagen	UR-701
Chemicals, peptides, and recombinant proteins
X-tremeGENE 9 DNA Transfection Reagent	Sigma-Aldrich	6365787001
Actinomycin D	Millipore Sigma	A1410-2MG
2′-Deoxyuridine 5′-triphosphate sodium salt (dUTP)	Millipore Sigma	D0184-25UMO
NEBNext Ultra II End Repair/dA-Tailing Module	NEB	E7546L
Instant Sticky-end Ligase Master Mix	NEB	M0370L
Thermolabile USER II Enzyme	NEB	M5508L
Critical commercial assays
Q5 Site-Directed Mutagenesis Kit	New England Biolabs	E0554S
Deposited data
EBOV NHP infection RNA-Seq reads	This study	GSE226106
Macaca fascicularis single-cell reference data	83	https://db.cngb.org/nhpca/download
RNA-seq data for healthy and diseased pancreatic islet samples	36	GSE50244
pancreatic islets scRNA-seq RNA-seq data	37	E-MTAB-5061
Peripheral blood data from the same EBOV-infected rhesus monkeys	18	GSE158390
Experimental models: Cell lines
HEK293T	ATCC	CRL-3216
U2OS	ATCC	HTB-96
Oligonucleotides
See Table S5		N/A
Recombinant DNA
See Table S5		N/A
Software and algorithms
Bulk RNA-seq Processing	This study	https://github.com/broadinstitute/EbolaNaturalHistory/
ternaDecov	This study	https://doi.org/10.5281/zenodo.8411808
STAR	84	https://github.com/alexdobin/STAR
python	Python core team	https://www.python.org/
R	R Core Team	https://www.r-project.org/
UMI-tools	85	https://github.com/CGATOxford/UMI-tools
BioMart	86	https://github.com/grimbough/biomaRt
viral-ngs	https://viral-ngs.readthedocs.io/en/latest/index.html	https://github.com/broadinstitute/viral-ngs
DESeq2	87	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
go.db.df	88	https://bioconductor.org/packages/release/data/annotation/html/GO.db.html
topGO	89	https://bioconductor.org/packages/release/bioc/html/topGO.html
ImpulseDE2	90	https://github.com/YosefLab/ImpulseDE2
MuSiC	32	https://xuranw.github.io/MuSiC/articles/MuSiC.html