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. Author manuscript; available in PMC: 2024 Nov 14.
Published in final edited form as: Immunity. 2023 Nov 2;56(11):2584–2601.e7. doi: 10.1016/j.immuni.2023.10.002

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
TotalSeq-A Human Universal Cocktail V1.0 BioLegend CAT # 399907; RRID: AB_2888692
TotalSeq-A CD30, clone BY88 BioLegend CAT # 333913; RRID: AB_2749966
TotalSeq-A CD197, clone G043H7 BioLegend CAT # 353247; RRID: AB_2750357
TotalSeq-A anti-human Hashtag 1 BioLegend CAT # 394601; RRID: AB_2750015
TotalSeq-A anti-human Hashtag 2 BioLegend CAT # 394603; RRID: AB_2750016
TotalSeq-A anti-human Hashtag 3 BioLegend CAT # 394605; RRID: AB_2750017
TotalSeq-A anti-human Hashtag 4 BioLegend CAT # 394607; RRID: AB_2750018
TotalSeq-A anti-human Hashtag 5 BioLegend CAT # 394609; RRID: AB_2750019
TotalSeq-A anti-human Hashtag 6 BioLegend CAT # 394611; RRID: AB_2750020
CD4-APC, clone OKT4 BioLegend CAT # 317416; RRID: AB_571945
HIV-1 core antigen-RD1, clone KC57 Beckman Coulter CAT # 6604667
IKZF3-BV421, clone 14C4C97 BioLegend CAT # 371010; RRID: AB_2616875
Ki67-BUV395, clone 56 BD Biosciences CAT # 564071
Bacterial and virus strains
NL4–3 NIH HIV Reagents Program CAT # ARP-114
10CB6 Ho et al.50 N/A
16CB3 Ho et al.50 N/A
20CB3 Ho et al.50 N/A
Biological samples
Blood samples from Sabes Cohort (Table S1) This study and Collora et al.40 N/A
Chemicals, peptides, and recombinant proteins
Digitonin 5% ThermoFisher CAT # BN2006
xGen Lockdown Reagents IDT CAT # 1072281
Protector RNase Inhibitor Sigma-Aldrich PN-3335399001
Human Cot-1 DNA Invitrogen CAT # 15279011
Dynabeads M-270 Streptavidin Invitrogen CAT # 65306
Human TruStain FcX BioLegend CAT # 422302; RRID: AB_2818986
LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit Thermo Fisher CAT # L10119
Human BD Fc Block BD Biosciences CAT # 564219
eBioscience Foxp3 / Transcription Factor Staining Buffer Thermo Fisher CAT # 00–5523-00
BD Pharmingen Purified Mouse Anti-Human CD3, Clone UCHT1 BD Biosciences CAT # 555330
BD Pharmingen™ Purified Mouse Anti-Human CD28, Clone CD28.2 BD Biosciences CAT # 556620
Recombinant Human Interleukin-2 Conn Stem CAT#C1002
Critical commercial assays
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle 10x Genomics PN-1000283
Chromium Nuclei Isolation Kit with RNase Inhibitor 10x Genomics PN-1000494
Chromium Next GEM Chip J Single Cell 10x Genomics PN-1000230
Dual Index Kit TT Set A 10x Genomics PN-1000215
Single Index Kit N Set A 10x Genomics PN-1000212
3’ Feature Barcode Kit 10x Genomics PN-1000262
EasySeq Dead Cell Removal Annexin V kit STEMCELL CAT # 17899
EasySep Human CD4+ T Cell Isolation Kit STEMCELL CAT # 17952
Memory CD4+ T cell Isolation Kit Miltenyi Biotec CAT # 130–091-893
Kapa Hifi Hotstart Readymix Kapa Biosystems CAT # KK2602
SPRIselect 5 mL reagent kit Beckman Coulter CAT # B23317
LIVE/DEAD Fixable Near-IR-Dead Cell Stain Kit Thermo Fisher L34975
Deposited data
DOGMAseq memory CD4+ T cells This study GEO: GSE239916
Oligonucleotides
ADT: * indicates phosphorothioate: CCTTGGCACCCGAGAATT*C*C Mimitou et al.27 DOGMAseq
HTO: * indicates phosphorothioate: GTGACTGGAGTTCAGACGTGTGC*T*C Mimitou et al.27 DOGMAseq
SIPCR: Dual index common primer for ADT/HTO This study, see Methods S1 DOGMAseq
RPX: Dual index common primer for ADT This study, see Methods S1 DOGMAseq
D7X: Dual index common primer for HTO This study, see Methods S1 DOGMAseq
Software and algorithms
CellRanger-Arc v2.0 10x Genomics https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/installation#download
CellRanger v5.0.1 10x Genomics https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
STAR v2.7 Dobin et al.57 https://github.com/alexdobin/STAR
Bowtie 2 v2.4.2 Langmead and Salzberg58 https://github.com/BenLangmead/bowtie2
Cutadapt v4.2 Martin59 https://cutadapt.readthedocs.io/en/stable/installation.html
Seqtk v1.3 https://github.com/lh3/seqtk https://anaconda.org/bioconda/seqtk
SAMtools v1.16.1 Li et al.60 https://anaconda.org/bioconda/samtools
IGV v2.16 Robinson et al.61 https://software.broadinstitute.org/software/igv/download
Seurat v4.3.0 Hao et al.62 https://cran.r-project.org/web/packages/Seurat/index.html
Signac v1.7 Stuart et al.63 https://cran.r-project.org/web/packages/Signac/index.html
Harmony v3.8 Korsunsky et al.64 https://portals.broadinstitute.org/harmony/articles/quickstart.html
Clustree v0.5.0 Zappia and Oshlack65 https://cran.r-project.org/web/packages/clustree/index.html
MACS3 v3.0.0 Zhang et al.66 https://github.com/macs3-project/MACS
EnsDb.Hsapiens.v86 v3.16 Rainer67 https://bioconductor.org/packages/release/data/annotation/html/EnsDb.Hsapiens.v86.html
BSgenome.Hsapiens.UCSC.hg38 v1.4.5 Team TBD68 https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg38.html
org.Hs.eg.db v3.8.2 Carlson et al.69 https://bioconductor.org/packages/release/data/annotation/html/org.Hs.eg.db.html
HOMER v4.11 Heinz et al.70 http://homer.ucsd.edu/homer/introduction/install.htsml
TFBSTools v3.16 Tan and Lenhard71 https://bioconductor.org/packages/release/bioc/html/TFBSTools.html
chromVAR v1.18 Schep et al.72 http://bioconductor.org/packages/release/bioc/html/chromVAR.html
JASPAR2022 Castro-Mondragon et al.73 https://bioconductor.org/packages/release/data/annotation/html/JASPAR2022.html
DSB v1.0.3 Mulè et al.74 https://cran.r-project.org/web/packages/dsb/index.html
ACAT v0.91 Liu et al.75 https://github.com/yaowuliu/ACAT
WGCNA v1.70 Langfelder and Horvath37 https://cran.r-project.org/web/packages/WGCNA/index.html
topGO v2.48 Alexa76 https://bioconductor.org/packages/release/bioc/html/topGO.html
fGSEA v1.22 Korotkevich et al.77 https://bioconductor.org/packages/release/bioc/html/fgsea.html
msigdbr v7.5.1 Dolgalev78 https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html
R version 4.0.5 R Core Team79 https://www.r-project.org/
FlowJo V10.8.1 FlowJo https://www.flowjo.com/solutions/flowjo/downloads
Analysis scripts This study https://doi.org/10.5281/zenodo.8351067