REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Brilliant Violet 650™ anti-human CD3, clone: OKT3	BioLegend	Cat# 317324; RRID: AB_2563352
Brilliant Violet 711™ anti-human CD4, clone: OKT4	BioLegend	Cat# 317440; RRID: AB_2562912
APC-Cyanine7™ anti-human CD14, clone: HCD14	BioLegend	Cat# 325620; RRID: AB_830693
Brilliant Violet 421™ anti-human PD-1, clone: EH12.1	BD Biosciences	Cat# 562516; RRID: AB_11153482
Brilliant Violet 785™ anti-human TIM-3, clone: F38-2E2	BioLegend	Cat# 345031; RRID: AB_2565833
C8 Monoclonal antibody (3B5) PE Texas Red, clone: 3B5	Invitrogen	Cat# MHCD0817; RRID: AB_10372359
Alexa Flour 700 anti-human CD3, clone: UCHT1	BioLegend	Cat# 300424; RRID: AB_493741
APC/Cyanine7 anti-human CD8, clone: SK1	BioLegend	Cat# 344714; RRID: AB_2044006
Alexa Flour 647 anti-human granzyme B, clone: GB11	BioLegend	Cat# 515406; RRID: AB_2566333
Brilliant Violet 421™ anti-human IL-17A, clone: BL168	BioLegend	Cat# 512322; RRID: AB_11218604
PE/Dazzle 549 anti-human IFN-γ, clone: 4S.B3	BioLegend	Cat# 502546; RRID: AB_2563627
MR1-6-FP (negative control)	NIH Tetramer Core Facility	–
MR1-5-OP-RU (mait-specific tetramer)	NIH Tetramer Core Facility	–
Biological samples
Whole Blood Samples	This Study	N/A
Whole BAL samples	This Study	N/A
BAL mononuclear cells (BLCs)	This Study	N/A
Peripheral blood mononuclear cells (PBMCs)	This Study	N/A
Chemicals, peptides, and recombinant proteins
Phorbol 12-myristate 13-acetate (PMA)	Sigma Aldrich	Cat no: 16561-29-8
Ionomycin	Sigma Aldrich	Cat no: 56092-82-1
Critical commercial assays
QuantiFERON-TB Gold Plus 2 Plates ELISA Kit	QIAGEN	Cat no: 622130
QuantiFERON-TB Gold Plus Blood Collection Tubes	QIAGEN	Cat no: 622536
Live/Dead Fixable Aqua Dead Cell Stain Kit	ThermoFisher Scientific	Cat no: L34957
Nextera XT DNA Sample Preparation Kit, 96 samples	Illumina	Cat no: FC-131-1096
Nextera XT Index Kit, 96 indices, 384 samples	Illumina	Cat no: FC-131-1002
PAXgene Blood RNA kit	QIAGEN	Cat no: 762174
PAXgene Blood RNA Tubes	BD Biosciences	Cat no: 762165
RNeasy Micro kit	QIAGEN	Cat no: E7490
NEBNext Poly(A) Mrna Magnetic Isolation Module	New England BioLabs	Cat no: E76005
NEBNext Multiplex Oligos for illumina	New England BioLabs	Cat no: E7490
NEBNext Ultra RNA Library Prep kit	New England BioLabs	Cat no: E7530
Deposited data
Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV	GEO (Whole transcriptomics)	GSE230738
Dysfunctional effector memory CD8 T cells in the bronchoalveolar compartment of people living with HIV	GEO (BAL-mini-population transcriptomics)	GSE231628
Oligonucleotides
Template switching oligonucleotides	IDT DNA	Customized
Reverse transcription DNA oligonucleotides	IDT DNA	Customized
Software and algorithms
Prism 10.2.3	GraphPad	NA
FlowJo 10.9.0	BD Biosciences	NA
Ingenuity Pathway Analysis version: 111725566	QIAGEN	https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
Transcriptional module R scripts	GitHub Biorepository	https://github.com/MJMurray1/MDIScoring)
RNASeqPipelineR (alignment, quantification and annotation of the RNA sequencing data)	GitHub Biorepository	https://github.com/RGLab/RNASeqPipelineR
STAR (v2.4.2a)	GitHub Biorepository	https://github.com/alexdobin/STAR
SARTools	GitHub Biorepository	https://github.com/PF2-pasteur-fr/SARTools
InnateDB (Gene Ontology Analysis)	InnateBD	https://www.innatedb.com/redirect.do?go=batchGo
Others
A HaemAtlas: characterizing gene expression in differentiated human blood cells	ArrayExpress	E-TABM-633, https://doi.org/10.1182/blood-2008-06-162958
Landscape of stimulation-responsive chromatin across diverse human immune cells	NCBI GEO	GSE117164, https://doi.org/10.1038/s41588-019-0505-9
IL-12 selectively programs effector pathways that are stably expressed in human CD8+ effector memory T cells in vivo	NCBI GEO	GSE27337, https://doi.org/10.1182/blood-2011-05-357111
A common transcriptomic program acquired in the thymus defines tissue residency of MAIT and NKT subsets	ArrayExpress	E-MTAB-7143, https://doi.org/10.1084/jem.20181483
Rapid synchronous type 1 IFN and virus-specific T cell responses characterize first wave non-severe SARS-CoV-2 infections.	ArrayExpress	E-MTAB-10022, https://doi.org/10.1016/j.xcrm.2022.100557