REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-HA-Biotin, High Affinity (3F10)	Millipore Sigma	Cat#12158167001 RRID:AB_390915
Streptavidin, R-Phycoerythrin Conjugate (SAPE) - 1 mg/mL	Fisher Scientific	Cat#S866A
CD45 Monoclonal Antibody (HI30), eFluor 450	eBioscience	Cat#48-0459-42 RRID:AB_2016677
Pacific Blue anti-human CD45 Antibody	BioLegend	Cat#304029, RRID:AB_2174123
Anti-human CD3 - PURE HU CD3 (OKT3)	Fisher Scientific	Cat#50-105-5018
Anti-human CD28 - IVR HU CD28 (CD28.2)	Fisher Scientific	Cat#50-105-4571
Goat Anti-Mouse antibody - IgG (H+L) Goat anti-Mouse	Fisher Scientific	Cat#PI-31160 RRID:AB_228297
Human-CD4 MicroBeads	Miltenyi Biotec	Cat#130-045-101
Bacterial and Virus Strains
NL-HA	Laboratory of Otto Yang28	N/A
Barcoded NL-HA	This paper	N/A
MegaX DH10B T1R cells	Thermo Fisher	Cat# C640003
Biological Samples
Human De-Identified Peripheral Blood Mononuclear Cells	UCLA Virology Core	N/A
Chemicals, Peptides, and Recombinant Proteins
SUW133	Laboratory of Paul Wender25	N/A
Raltegravir	Merck	N/A
Tenofovir disoproxil fumarate (TDF)	Gilead Sciences	N/A
Emtricitibine (FTC)	Gilead Sciences	N/A
Critical Commercial Assays
Perkin Elmer Alliance HIV-1 p24 kits	Perkin Elmer	Cat#NEK050
Deposited Data
Raw sequencing reads deposited on SRA (Short Read Archive) database	This study	Accession number: PRJNA562389
Experimental Models: Cell Lines
293FT cells	Invitrogen	Cat#R70007 RRID:CVCL_6911
GHOST (3) CXCR4+CCR5+	NIH AIDS Reagent Program	Cat#3942
CEM CD4+ Cells	NIH AIDS Reagent Program	Cat#117
Experimental Models: Organisms/Strains
Mouse: NSG: PrkdcscidIl2rgtm1wjl	The Jackson Laboratory	Stock#005557 RRID:IMSR_JAX:005557
Oligonucleotides
See Table S2 for List of Oligonucleotide sequences	N/A	N/A
Software and Algorithms
Codes	This study	https://github.com/Tian-hao/BarcodeHIV
FlowJo (v7)	FlowJo, LLC	N/A
Prism 6	GraphPad	N/A
Excel	Microsoft	N/A
Other
Phusion High-Fidelity DNA Polymerase	ThermoFisher	Cat#F530L
NEBNext Ultra II DNA Library Prep Kit for Illumina	New England Biolabs	Cat#E7645
RNeasy minikit	QIAGEN	Cat#74104
QIAamp Viral RNA Mini Kit	QIAGEN	Cat# 52904
One-Step RT-PCR kit	Bioland Scientific	Cat#RT01-01
SuperScript IV First-Strand Synthesis System	ThermoFisher	Cat#18091050
RNA clean and concentrator kit	Zymo Research	Cat#R1017
DNA clean and concentrator kit	Zymo Research	Cat#D4033