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 CD4 Alexa Fluor 700 (Clone RPAT4) |
BD |
Cat# 557922; RRID: AB_396943 |
Mouse anti-human CD4 PerCP-Cy5.5 (Clone RPAT4) |
BioLegend |
Cat# 300530; RRID: AB_893328 |
Mouse anti-human CD3 Pacific Blue (Clone UCHT1) |
BD |
Cat# 558117; RRID: AB_397038 |
Mouse anti-human CCR6 PE (Clone 11A9) |
BD |
Cat# 559562; RRID: AB_397273 |
Mouse anti-human CCR5 PE (Clone 2D7/CCR5) |
BD |
Cat# 555993; RRID: AB_396279 |
Mouse anti human IFN-γ Alexa Fluor 700 (Clone B27) |
BD |
Cat# 557995; RRID: AB_396977 |
Mouse anti human CXCR4 APC (Clone 12G5) |
Thermo Fisher |
Cat# 17–9999–42; RRID: AB_1724113 |
Mouse anti human Ki67 BV421 (Clone B56) |
BD |
Cat# 562899; RRID: AB_2686897 |
Rat anti human Integrinβ7 PE-Cy 5 (Clone FIB504) |
BD |
Cat# 551059; RRID: AB_394026 |
Mouse anti human CD56 FITC (Clone HCD56) |
eBioscience |
Cat# 318304; RRID: AB_604100 |
Mouse anti human IL-17A PE (Clone eBio64DEC17) |
eBioscience |
Cat# 12–7179–42; RRID: AB_1724136 |
Mouse anti human IL-22 PE-Cyanine7 (Clone 22URTI) |
eBioscience |
Cat# 25–7229–42; RRID: AB_10853346 |
Mouse anti human CD8 FITC (Clone BW135/80) |
Miltenyi Biotech |
Cat# 130–080–601; RRID: AB_244336 |
Mouse anti human CD19 FITC (Clone LT19) |
Miltenyi Biotech |
Cat# 130–091–328; RRID: AB_244222 |
Mouse anti human CD45RA APCeFluor780 (Clone HI100) |
eBioscience |
Cat# 47–0458–42; RRID: AB_10853641 |
LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (405 nm excitation) |
Invitrogen |
Cat# L34957
|
Rabbit anti human AhR |
Abcam |
Cat# ab190797; RRID: AB_2894707 |
Rabbit anti human AhR |
Cell Signaling |
Cat# 83200; RRID: AB_2800011 |
Rabbit anti human ARNT |
Cell Signaling |
Cat# 5537; RRID: AB_10694232 |
Normal Rabbit IgG |
Cell Signaling |
Cat# 2729; RRID: AB_1031062 |
Monoclonal anti-βActin (clone AC15) |
Sigma |
Cat# A5441; RRID: AB_476744 |
|
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 Roger J Pomerantz (Thomas Jefferson University, Philadelphia, Pennsylvania, USA) and Dr. Michel J. Tremblay (Université Laval, Québec City, QC, Canada) |
N/A |
|
Biological samples |
|
Leukaphereses of ART treated and untreated people living with HIV |
Recruited at the Montreal Chest Institute, McGill University Health Center and Center Hospitalier de l’Université de Montréal via the collaboration of Dr Jean-Pierre Routy’s group |
N/A |
|
Chemicals, peptides, and recombinant proteins |
|
Dulbecco’s Modified Eagle’s medium (DMEM) |
Thermo Fisher |
Cat# 11995065 |
Roswell Park Memorial Institute (RPMI) |
Thermo Fisher |
Cat# 11875–093 |
Penicillin/Streptomycin |
Gibco |
Cat# 15140–122 |
Fetal Bovine Serum (FBS) |
Sigma |
Cat# F2442 |
Bovine Serum Albumin (BSA) |
BioShop |
Cat# ALB001 |
Phosphate Buffered Saline (PBS) |
Thermo Fisher |
Cat# 20012050 |
Tween 20 |
Thermo Fisher |
Cat# BP337–500 |
PVDF membrane |
Millipore Sigma |
Cat# ISEQ00010 |
RIPA Buffer 10X |
NEB |
Cat# 9806S |
rhIL-2 |
R&D Systems |
Cat# 202–IL–050 |
rhIL-10 |
R&D Systems |
Cat# 217–IL |
rhIL-22 |
R&D Systems |
Cat# 782–IL–010 |
CH-223191 |
Sigma |
Cat# C8124 |
FICZ |
Sigma |
Cat# SML1489 |
DNAzol™ Reagent |
Invitrogen |
Cat# 10503027 |
T7 Endonuclease I - 250 units |
NEB |
Cat# M0302S |
Phusion® High-Fidelity DNA Polymerase |
NEB |
Cat# M0530S |
UltraComp ebeads |
eBioscience |
Cat# 01–2222–42 |
Formaldehyde 37% |
Sigma |
Cat#F79500 |
LC480 probe master mix |
Roche |
Cat# 4707494001 |
Amersham ECL Prime Western Blotting System |
Cytiva |
Cat# RPN2232 |
Brefeldin A |
Sigma |
Cat# B7651 |
PMA |
Sigma |
Cat# P1585 |
Ionomycin |
Sigma |
Cat# I0634 |
Luna Universal qPCR Master Mix |
NEB |
Cat# M3003E |
TMB Peroxidase Substrate |
Fitzgerald |
Cat# 42R–TB102 |
Streptavidin Poly-HRP40 |
Fitzgerald |
Cat# 65R–S104PHRP–200UG |
|
Critical commercial assays |
|
Memory CD4+ T cell Isolation Kit, human |
Miltenyi |
Cat#130–091–893 |
Fixation/Permeabilization Solution Kit (Cytofix/Cytoperm) |
BD |
Cat# 554714 |
Human IL-10 DuoSet ELISA |
R&D Systems |
Cat# DY217B |
Human IL-17A (homodimer) ELISA Ready-SET-Go |
Thermo Fisher |
Cat# 88–7176–86 |
Human IL-22 DuoSet ELISA |
R&D Systems |
Cat# DY782 |
Human IFN-γ ELISA |
Thermo Fisher |
Cat# 88–7316–86 |
QuantiTect SYBR Green RT-PCR Kit |
Qiagen |
Cat# 204245 |
Human T cell Nucleofector® Kit |
Lonza |
Cat# VPA–1002 |
Rneasy Plus Mini Kit |
Qiagen |
Cat# 74136 |
CHIP assay kit |
EMD Millipore |
Cat# 17–295 |
Luna® Universal qPCR Master Mix |
NEB |
Cat# M3003S |
MyTaq Extract PCR kit |
Bioline |
Cat# BIO–21126 |
High-fidelity enzyme Q5 |
NEB |
Cat# M0530L |
QIAEX II Gel extraction kit |
Qiagen |
Cat# 20021 |
GeneJET PCR Purification Kit |
Thermo Fisher |
Cat# K0702 |
|
Deposited data |
|
RNA-Sequencing dataset |
This paper |
GEO: GSE198078
|
Original western blot images relative to Figures 1, S1 and S2. |
This paper; Mendeley Data |
https://data.mendeley.com/datasets/4ry9gxv7tp/1
|
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 |
|
ACH-2 cell line |
NIH HIV Reagent Program |
Cat# ARP–349 |
293T cells |
ATCC |
Cat# CRL–3216 |
TZM-bl cells |
NIH HIV Reagent Program |
Cat# ARP–8129 |
HIV-p24 Abs producing hybridome |
From Dr. Michel J. Tremblay (Université Laval, Québec City, QC, Canada) |
N/A |
|
Oligonucleotides |
|
See Table S3: Oligonucleotides |
This paper |
N/A |
|
Software and algorithms |
|
Kallisto software version 0.44.0 |
Pachter Lab |
https://pachterlab.github.io/kallisto/
|
FlowJo version 10 |
BD |
https://www.flowjo.com/
|
GraphPad Prism 7 |
GraphPad |
https://www.graphpad.com/
|
Microsoft Excel v16 |
Microsoft Office |
https://www.microsoft.com/en-ca/microsoft-365/excel
|
Snapgene software |
Snapgene |
https://www.snapgene.com/
|
TIDE software |
Tide |
https://tide.nki.nl/
|
ICE software |
Synthego |
https://ice.synthego.com/
|
QuantStudio™ Design & Analysis Software |
Thermo Fisher |
https://www.thermofisher.com/
|