Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy

. 2023 Jan 11;31(1):83–96.e5. doi: 10.1016/j.chom.2022.12.002

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

PBMC samples from study participants living with HIV	This study, Massachusetts General Hospital, University of California at San Francisco, Case Western Reserve University, National Institutes of Health (NIH) Clinical Center	N/A

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
PHA	ThermoFisher Scientific	Cat#R30852701
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
Britelite plus Reporter Gene Assay System	PerkinElmer	Cat#6066761
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	Roadmap Epigenomics et al.³⁴	http://www.roadmapepigenomics.org/
ENCODE database	National Human Genome Research Institute, 2012	https://www.encodeproject.org/
Hi-C data from CD4 T cells	Einkauf et al.⁸	GEO ID: GSE168337
RNA-Seq data from CD4 T cells	Jiang et al.⁹	GEO ID: GSE 144334

Oligonucleotides

See Table S4 for List of Primers/Probes	Einkauf et al.⁸ and Jiang et al.⁹	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.¹²	https://github.com/BWH-Lichterfeld-Lab/Intactness-Pipeline
Los Alamos National Laboratory (LANL) HIV Sequence Database Hypermut 2.0	Rose and Korber⁵⁸	https://www.hiv.lanl.gov/content/sequence/HYPERMUT/background.html
MUSCLE	Edgar⁵⁹	http://www.drive5.com/muscle/
Geneious Prime 2021.0.3	Biomatters	https://www.geneious.com/download/
bwa-mem	Li and Durbin⁶⁰	http://maq.sourceforge.net/
RepeatMasker	Institute for Systems Biology	http://www.repeatmasker.org/
STAR aligner software	ENCODE, version 2.5.1b	https://www.encodeproject.org/software/star/
Prism	Graphpad, version 8.2.1	https://www.graphpad.com/scientific-software/prism
R	R Core Team and R Foundation for Statistical Computing, version 3.5.3	https://www.r-project.org
FastQC	Babraham Bioinformatics, version 0.11.	https://www.bioinformatics.babraham.ac.uk
Samtools	Genome Research Limited, version 1.14	http://www.htslib.org
MACS2	MACS3 project team, version 2.1.1.20160309	https://github.com/macs3-project/MACS
Recombinant Identification Program	Los Alamos National Laboratory	https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html
Bowtie2	Langmead and Salzberg,⁶¹ version 2.2.9	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Python	Python Software Foundation, version 3.9	https://www.python.org/
Omixon HLA Explore	Omixon, version beta	https://www.omixon.com/products/hla-explore/
Biorender	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
Fluidigm Access Array	Fluidigm	https://www.standardbio.com/products-services/instruments/access-array
NextSeq 500 Instrument	Illumina	https://www.illumina.com/systems/sequencing-platforms/nextseq.html