REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Purified NA/LE Mouse Anti-Human CD3 (Clone UCHT1)	BD	Cat#555329; RRID: AB_395736
Purified NA/LE Mouse Anti-Human CD28 (Clone CD28.2)	BD	Cat#555725; RRID: AB_396068
HIV-1 core (p24) antigen-FITC (Clone KC57)	Beckman Coulter	Cat#6604665; RRID: AB_1575987
Mouse anti-human CD3 Alexa 700 (Clone UCHT1)	BD	Cat# 557943; RRID: AB_396952
Mouse anti-human CD3 Pacific Blue (Clone UCHT1)	BD	Cat#558117; RRID: AB_397038
Mouse anti-human CD317 BV421 (BST2, Clone Y129)	BD	Cat#566381; RRID: AB_2744363
Mouse anti-human CD4 PerCP-Cy5.5 (Clone RPA-T4)	Biolegend	Cat#300530; RRID: AB_893322
Rabbit polyclonal anti-BST2	Provided by Dr. Éric A. Cohen (IRCM, Montreal, QC, Canada (Dube et al., PlosPathogens, 2010)
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (405 nm excitation)	Invitrogen	Cat#L34957
Goat polyclonal Secondary Antibody to Rabbit IgG - Fc Alexa Fluor 594	Abcam	Cat#ab150092; RRID:AB_2893495
Bacterial and virus strains
HIV-1 THRO plasmid (pTHRO.c/2626), subtype B	NIH AIDS Reagent Program (Contribution of Dr. John Kappes and Dr. Christina Ochsenbauer)	Cat#11745
NL4.3BaL HIV plasmid	From Dr. Dana Gabuzda (Dana-Farber Cancer Institute, Boston, MA, USA)	N/A
Biological samples
Leukaphereses of ART treated and untreated people living with HIV	Recruited at the Montreal Chest Institute, McGill University Health Centre and Centre Hospitalier de l’Université de Montréal with the help of Dr Jean-Pierre Routy’s group	N/A
Chemicals, Peptides, and Recombinant Proteins
rhIL-2	R&D Systems	Cat#202-IL-050
rhIL-17A	R&D Systems	Cat#7955-IL-025
rhTNF-α	R&D Systems	Cat#210-TA-020
Recombinant Viral B18R Protein	R&D Systems	Cat#8185-BR-025
rhCCL20	R&D Systems	Cat#360-MP-025
Critical commercial assays
Memory CD4+ T Cell Isolation Kit, human	Miltenyi	Cat#130-091-893
Fixation/Permeabilization Solution Kit (Cytofix/Cytoperm)	BD	Cat#554714
p24 ELISA	Homemade. Hybridome provided by Dr. Michel J. Tremblay (Bounou et al., J Virol., 2002)
Human CCL20/MIP-3 alpha DuoSet ELISA	R&D Systems	Cat#DY360-05
Human IL-8/CXCL8 DuoSet ELISA	R&D Systems	Cat#DY208-05
SmGM- 2 Smooth Muscle Cell Growth Medium -2 BulletKit	Lonza	Cat#CC-3182
QuantiTect SYBR Green RT-PCR Kit	Qiagen	Cat #204245
AllPrep DNA/RNA/miRNA Universal kit	Qiagen	Cat#80224
Rneasy Plus Mini Kit	Qiagen	Cat#74136
Deposited data
RNA-Sequencing data set	This paper	GEO: GSE147045
Gene Ontology: Biological Processes database	Broad Institute	https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=BP
Homo Sapiens database GRCh 37 version75	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13/
Experimental models: cell lines
HT-29 cell line	ATCC	Cat#HTB-38; RRID:CVCL_0320
HEK-Blue™ IFN-α/β Cells	InvivoGen	Cat#hkb-ifnab
Human Intestinal Epithelial Cells (inEpC)	Lonza	Cat#CC-2931, Lot 0000751353
ACH-2 cell line	NIH HIV Reagent Program	Cat#ARP-349; RRID:CVCL_0138
Oligonucleotides
See Table S1: Oligonucleotides
Software and algorithms
Kallisto software version 0.44.0	Pachter Lab	https://pachterlab.github.io/kallisto/
R, pheatmap package	The R Foundation	https://CRAN.R-project.org/package=pheatmap
FlowJo version 10	BD	https://www.flowjo.com/
GraphPad Prism 7	GraphPad	https://www.graphpad.com/
Cytoscape 3.7.2	National Resource for Network Biology	https://cytoscape.org/
ClueGO	National Resource for Network Biology	https://apps.cytoscape.org/apps/cluego