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. Author manuscript; available in PMC: 2022 Dec 13.
Published in final edited form as: Cell Rep. 2022 Apr 26;39(4):110739. doi: 10.1016/j.celrep.2022.110739

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
CD4 neg selection kit for IMag: human CD4 T cell BD Biosciences Cat#557939; RRID: AB_2802162
Anti-human CD3 BB BD Biosciences Cat#564465; RRID: AB_2744386
Anti-human CD8 PeCy7 BD Biosciences Cat#557746; RRID: AB_396852
Anti-human CD45 PerCPCy5.5 BD Biosciences Cat#564105; RRID: AB_2744405
Anti-human CD45 RO PE BD Biosciences Cat#555493; RRID: AB_395884
Anti-human CD45 RO PerCPCy5.5 BD Biosciences Cat#560607; RRID: AB_1727500
Anti-human CD45 RA APC BD Biosciences Cat#550855; RRID: AB_398468
Anti-human CD27 APC BD Biosciences Cat#561400; RRID: AB_10645790
Anti-human CD197 (CCR7) PE BD Biosciences Cat#560765; RRID: AB_2033949
Viability stain 780 BD Biosciences Cat#565388; RRID: AB_2869673
Biological samples
Patient derived PBMCs (HIV-STAR) Ghent University Hospital N/A
Patient derived Plasma (HIV-STAR) Ghent University Hospital N/A
Chemicals, peptides, and recombinant proteins
Proteinase K 20mg/mL Ambion/Lifetechnologies Cat#AM2546
Ultrapure 1M TrisHCL PH 8 Thermo Fisher Scientific Cat#15568-025
Nonidet P 40 Substitute solution Sigma Aldrich Cat#98379
Tween-20 Sigma Aldrich Cat#P9416
PBS, pH 7.2 Thermo Fisher Scientific Cat#20012027
dNTP PCR nucleotide mix 10 mM 1mL Promega Cat#C1145
UltraPure DNase/RNAse-free water Thermo Fisher Scientific Cat#10977023
RNAse inhibitor Takara Cat#2313B
ThermaSTOP RT Sigma Aldrich Cat#TSTOPRT-250
RNAse H Invitrogen Cat#18080051
PrimeStar GXL polymerase Takara Cat#R050B
ThermaStop Sigma Aldrich Cat#TSTOP-500
AMPure XP Beckman Coulter Cat#A63880
Critical commercial assays
REPLI-g single cell kit Qiagen Cat#150345
MyTaq DNA polymerase Bioline #BIO-21105
QIAamp Viral RNA Mini Kit Qiagen Cat#52904
SuperScript III First Strand synthesis system Invitrogen Cat#18080051
Quant-iT PicoGreen dsDNA Assay Kit Invitrogen Cat#P11496
Nextera XT DNA Library Preparation Kit Illumina FC-131-1096
Nextera XT Index Kit v2 Set A Illumina FC-131-2001
MiSeq Reagent Kit v2 (300-cycles) Illumina MS-102-2002
Deposited data
RNA and DNA sequencing – V1-V3 env SGS data GenBank GenBank:MH639149–MH643573
RNA and DNA sequencing – V1-V3 env SGS data GenBank GenBank:MH648157–MH648606
RNA and DNA sequencing – FLIPS NFL data GenBank GenBank:MZ041268–MZ041657
RNA and DNA sequencing – 5′ and 3′ end plasma data GenBank GenBank:MZ955650–MZ955856
Oligonucleotides
See Table S7 for a list of used oligonucleotides.
Software and algorithms
Flow Jo software BD Biosciences https://www.flowjo.com/
ddpcRquant software Trypsteen et al., 2015 http://statapps.ugent.be/dPCR/ddpcrquant/
‘Integration Sites’ webtool Mullins Lab https://indra.mullins.microbiol.washington.edu/integrationsites/
De novo assembly pipeline Cole et al., 2021 https://github.com/laulambr/virus_assembly
FastQC Babraham Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc
bbmap BBMap sourceforge.net/projects/bbmap/
MEGAHIT Li et al., 2015 https://github.com/voutcn/megahit
MAFFT Katoh et al., 2002 https://mafft.cbrc.jp/alignment/software/
MEGA7 Kumar et al., 2016 https://www.megasoftware.net/
DualBrothers Minin et al., 2005 https://msuchard.faculty.biomath.ucla.edu/DualBrothers/index.html#:~:text=DualBrothers%20is%20a%20recombination%20detection,in%20a%20multiple%20sequence%20alignment
Recombinant Identification Program Los Alamos HIV Database https://www.hiv.lanl.gov
PhyML v3.0 Guindon et al., 2010 https://github.com/stephaneguindon/phyml/
iTOL v5 Letunic and Bork, 2019 https://itol.embl.de/
R version 3.6.2 R Core Team, 2020 https://www.R-project.org/
Companion to Applied Regression, “car” R package https://cran.r-project.org/web/packages/car/index.html
Other
BD FACSJazz BD Biosciences Cat#655490
QX200 Droplet Digital PCR System Biorad Cat#1864001
QX200 Droplet Generator Biorad Cat#1864002
MiSeq System Illumina Cat#SY-410-1003