REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse antihuman CD4 (clone RPA-T4)	BioLegend	Cat#300518; RRID: AB_314086
Mouse antihuman CD3 (clone OKT3)	BioLegend	Cat#317332; RRID: AB_2561943
Mouse antihuman CD45RO (clone UCHL1)	BioLegend	Cat#304236; RRID: AB_2562107
Mouse antihuman CCR7 (clone G043H7)	BioLegend	Cat#353216; RRID: AB_10916386
Biological samples
PBMC samples from study participants living with HIV	Massachusetts General Hospital	https://www.massgeneral.org/
Chemicals, peptides, and recombinant proteins
Buffer RLT Plus	Qiagen	Cat#1053393
Invitrogen Dynabeads MyOne Streptavidin C1	ThermoFisher Scientific	Cat#65002
Invitrogen SUPERase⋅In RNase Inhibitor	ThermoFisher Scientific	Cat#AM2694
Invitrogen dNTP mix (10mM each)	ThermoFisher Scientific	Cat#18427088
AMPure XP beads	Beckman Coulter	Cat#A63882
5M NaCl	ThermoFisher Scientific	Cat#AM9760G
10M NaOH	Millipore Sigma	Cat#72068
0.5M EDTA (pH 8.0)	Promega	Cat#V4231
UltraPure 1M Tris-HCI Buffer (pH 7.5)	ThermoFisher Scientific	Cat#15567027
1M MgCl2	ThermoFisher Scientific	Cat#AM9530G
2M KCl	ThermoFisher Scientific	Cat#AM9640G
1M DTT	Millipore Sigma	Cat#646563
TWEEN 20 (50% Solution)	ThermoFisher Scientific	Cat#003005
Betaine solution (5M)	Millipore Sigma	Cat#B0300
BioLegend Cell Activation Cocktail (without Brefeldin A)	BioLegend	Cat#423302
Recombinant IL-2	NIH AIDS Reagent program	www.hivreagentprogram.org
AZT	NIH AIDS Reagent Program	www.hivreagentprogram.org
Critical commercial assays
DNeasy Blood and Tissue Kit	Qiagen	Cat#69504
ddPCR Supermix for Probes (No dUTP)	Bio-Rad	Cat#1863024
Invitrogen SuperScript II Reverse Transcriptase kit	ThermoFisher Scientific	Cat#18064022
KAPA HiFi HotStart ReadyMix	Roche	Cat#7958935001
REPLI-g Single Cell Kit	Qiagen	Cat#150345
REPLI-g Advanced Single Cell Kit	Qiagen	Cat#150365
Invitrogen Platinum Taq DNA Polymerase High Fidelity	ThermoFisher Scientific	Cat#11304102
Stemcell EasySep Human CD4+ T Cell Isolation Kit	Stemcell Technologies	Cat#17952
PicoPure RNA Isolation Kit	Applied Biosystems	Cat#0204
Deposited data
Ensembl (v86)	Ensembl	http://oct2016.archive.ensembl.org/index.html
UCSC Genome Browser	UCSC	http://genome.ucsc.edu
GENCODE (v32)	GENCODE	https://www.gencodegenes.org/human/release_32.html
Roadmap database	Kundaje et al., 2015	http://www.roadmapepigenomics.org/
ENCODE database	(ENCODE Project Consortium, 2012)	https://www.encodeproject.org/
iMethyl database	Komaki et al., 2018	http://imethyl.iwate-megabank.org/
Hi-C data from CD4 T cells	This study	GEO ID: GSE168337
ATAC-Seq and RNA-Seq data from CD4 T cells	Jiang et al., 2020	GEO ID: GSE144334
Oligonucleotides
See Table S3 for List of Primers/Probes	Millipore Sigma/IDT/Qiagen	N/A
Quantitative Synthetic Human immunodeficiency virus 1 (HIV-1) RNA	ATCC	Cat#VR-3245S
Software and algorithms
QuantaSoft software	Bio-Rad	Cat#1864011
Ultracycler v1.0	Seed and Wang, personal communication	https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/viral_genome_sequencing_pages/viral_genome_sequencing_data.jsp
Automated in-house proviral intactness bioinformatic pipeline in Python	Lee et al., 2017	https://github.com/BWH-Lichterfeld-Lab/Intactness-Pipeline
Los Alamos National Laboratory (LANL) HIV Sequence Database Hypermut 2.0	Rose and Korber, 2000	https://www.hiv.lanl.gov/content/sequence/HYPERMUT/background.html
ProSeq-IT	Shao et al., 2020	https://psd.cancer.gov/tools/pvs_annot.php
MUSCLE	Edgar, 2004	http://www.drive5.com/muscle/
Geneious Prime 2021.0.3	Biomatters	https://www.geneious.com/download/
bwa-mem	Li and Durbin, 2009	http://maq.sourceforge.net/
RepeatMasker	Institute for Systems Biology	http://www.repeatmasker.org/
RSEM (v1.2.22)	Li and Dewey, 2011	http://deweylab.github.io/RSEM/
STAR aligner software (2.5.1b)	ENCODE	https://www.encodeproject.org/software/star/
Prism	Graphpad, https://www.graphpad.com/scientific-software/prism	version 8.2.1
R	R Core Team and R Foundation for Statistical Computing, https://www.r-project.org	version 3.5.3
FastQC	Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk	version 0.11.9
Samtools	Genome Research Limited, http://www.htslib.org	version 1.14
MACS2	https://github.com/macs3-project/MACS	version 2.1.1.20160309
Recombinant Identification Program	Los Alamos National Laboratory, https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html
Bowtie2	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	version 2.2.9
Homer	http://homer.ucsd.edu/homer/interactions/	version 4.10.3
FitHiC2	https://bioconductor.org/packages/release/bioc/html/FitHiC.html	version 1.20.0
FIREcaller	https://github.com/yycunc/FIREcaller	version 1.40
Python	Python Software Foundation, https://www.python.org/	version 3.9
Scikit-learn	https://scikit-learn.org/	Version 0.24.0
Biorender	https://biorender.com
Other
QX200 Droplet Digital PCR System	Bio-Rad	https://www.bio-rad.com/en-us/life-science/digital-pcr/qx200-droplet-digital-pcr-system
C1000 Touch Thermal Cycler with 96-Well Fast Reaction Module	Bio-Rad	Cat#1851196
Quantify One and ChemiDoc MP Image Lab	Bio-Rad	https://www.bio-rad.com/en-us/product/chemidoc-mp-imaging-system
ThermoMixer C	Eppendorf	Cat#5382000023
96-Well PCR Post Magnet Low Elution Plate	Permagen	Cat#LE400
DynaMag-96 Side Skirted Magnet	ThermoFisher Scientific	Cat#12027
DynaMag-2 Magnet	ThermoFisher Scientific	Cat#12321D
Illumina MiSeq performed by MGH CCIB DNA Core facility	Illumina/MGH CCIB DNA Core	https://dnacore.mgh.harvard.edu/new-cgi-bin/site/pages/index.jsp
FACS Aria Cell Sorter	BD Biosciences	https://www.bdbiosciences.com/en-us/products/instruments/flow-cytometers/research-cell-sorters/bd-facsaria-iii
NextSeq 500 Instrument	Illumina	https://www.illumina.com/systems/sequencing-platforms/nextseq.html