REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-ISG15	Atlas Antibodies	Cat#HPA004627, RRID: AB_1079152
Rabbit polyclonal anti-GP2	Thermo Fisher	Cat#PA5-42593, RRID: AB_2608499
Biological Samples
Human PBMC from the ACTU-3500 trial	This paper	N/A
Human whole blood from the ACTU-3500 trial	This paper	N/A
Human rectal biopsies from the ACTU-3500 trial	This paper	N/A
Human duodenal biopsies from the ACTU-3500 trial	This paper	N/A
Human PBMC from GMS A	This paper	N/A
Human cervical biopsies from GMS A	This paper	N/A
Human vaginal biopsies from GMS A	This paper	N/A
Human PBMC from GMS B	This paper	N/A
Human rectal biopsies from MTN-017	This paper	N/A
Critical Commercial Assays
HumanHT-12 v4 Expression BeadChips	Illumina	N/A (discontinued)
Ovation PicoSL WTA System V2 kit and Encore BiotinIL kit	NuGEN/TECAN	Cat#3302-12, Cat#4210-48
Illumina TotalPrep RNA Amplification kit	Thermo Fisher	Cat#AMIL1791
qScript cDNA Synthesis Kit	QuantaBio	Cat#95047-025
ddPCR Supermix for Probes (no dUTP)	Bio-Rad	Cat#186-3024
TruSeq Stranded Total RNA with Ribo-Zero Globin kit	Illumina	Cat#20020612
Deposited Data
Microarray data from the ACTU-3500 trial (effect of oral TDF/FTC on gene expression in the blood, duodenum, and rectum)	This paper	GEO: GSE139611
Microarray data from MTN-017 (effect of oral TDF/FTC or topical rectal 1% tenofovir gel on gene expression in the rectum)	This paper	GEO: GSE138723
Microarray data from GMS A (effect of oral TDF/FTC or oral TDF on gene expression in the blood, cervix, and vagina)	This paper	GEO: GSE139655
Microarray data from GMS B (effect of oral TDF/FTC or oral TDF on gene expression in the blood as compared to placebo)	This paper	GEO: GSE139411
RNaseq data from MTN-017 (effect of oral TDF/FTC or topical rectal 1% tenofovir gel on gene expression in the rectum)	This paper	https://doi.org/10.6084/m9.figshare.c.4704827.v2
Mass spectrometry-based proteomics data from MTN-017 (effect of oral TDF/FTC on gene expression in the rectum)	This paper	https://doi.org/10.6084/m9.figshare.c.4704827.v2
ddPCR data from ACTU-3500, MTN-017, and GMS A (effect of oral TDF/FTC or oral TDF on gene expression in the blood, cervix, duodenum, rectum, and vagina)	This paper	https://doi.org/10.6084/m9.figshare.c.4704827.v2
Oligonucleotides
Primers/probes for ddPCR	IDT	Table S2
Software and Algorithms
lumi package	38	https://www.bioconductor.org/packages/release/bioc/html/lumi.html
limma package	39	https://www.bioconductor.org/packages/release/bioc/html/limma.html
R	CRAN	https://cran.r-project.org/
Tidyverse	CRAN	https://cran.r-project.org/web/packages/tidyverse/index.html