REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti-human c-kit, clone CL1657	Novus Biologicals	Cat# NBP2-52975
Mouse anti-human tryptase, clone AA1	Abcam	Cat# ab2378; RRID: AB_303023
Mouse anti-human CD11c, clone 5D11	Leica Biosystems	Cat# CD11C-563-L-CE; RRID: AB_2750846
Rabbit anti-human CD20, polyclonal	ThermoFisher	Cat# RB-9013; RRID: AB_149767
Rabbit anti-human CD3, polyclonal	Dako Omnis	Cat# GA503
Donkey anti-rabbit IgG Alexa Fluor 647	Jackson ImmunoResearch Laboratories	Cat# 711-605-152; RRID: AB_2492288
Donkey anti-rabbit IgG Alexa Fluor 488	ThermoFisher	Cat# A32790; RRID: AB_2866495
Donkey anti-rabbit IgG Alexa Fluor 546	ThermoFisher	Cat# A10040; RRID: AB_2534016
Goat anti-mouse IgG1 Alexa Fluor 546	ThermoFisher	Cat# A21123; RRID: AB_2535765
Anti-rabbit IgG Alexa Fluor 488	ThermoFisher	Cat# Z25302; RRID: AB_2572214
Anti-rabbit IgG Alexa Fluor 546	ThermoFisher	Cat# Z25304; RRID: AB_2736947
Donkey anti-mouse IgG Alexa Fluor 488	ThermoFisher	Cat# A-21202; RRID: AB_141607
Mouse anti-human CD3, clone SP34-2	BD Biosciences	Cat# 551916; RRID: AB_394293
Mouse anti-human CD4, clone L200	BD Biosciences	Cat# 551980; RRID: AB_398521
Mouse anti-human CD8a, clone RPA-T8	BD Biosciences	Cat# 563823; RRID: AB_2687487
Mouse anti-human CD8b, clone 2ST8.5H7	BD Biosciences	Cat# 641058; RRID: AB_1645723
Mouse anti-human TCR gamma/delta, clone 5A6.E9	Invitrogen	Cat# TCR1061; RRID: AB_223500
Mouse anti-human CD16, clone 3G8	BD Biosciences	Cat# 556617; RRID: AB_396489
Mouse anti-human NKG2A, clone Z199	Beckman Coulter	Cat# A60797; RRID: AB_10643105
Mouse anti-human Granzyme B, clone GB11	BD Biosciences	Cat# 561998; RRID: AB_10894005
Mouse anti-human Granzyme A, clone CB9	BD Biosciences	Cat# 557449; RRID: AB_396712
Mouse anti-human Granzyme K, clone G3H69	BD Biosciences	Cat# 566655; RRID: AB_2869812
Bacterial and virus strains
M. tuberculosis: Erdman strain	Flynn Lab	N/A
Biological samples
Cynomolgus macaque granulomas	This study	N/A
Human granulomas	This study	N/A
Chemicals, peptides, and recombinant proteins
2-mercaptoethanol	Sigma	Cat# M3148
Buffer RLT	QIAGEN	Cat# 79216
Buffer RLT Plus	QIAGEN	Cat# 1053393
Deoxynucleotide (dNTP) solution mix	NewEngland BioLabs	Cat# N0447L
Superase.In RNase Inhibitor	Thermo Fisher	Cat# AM2696
Maxima H minus reverse transcriptase	Fisher Scientific	Cat# EP0753
AMPure XP beads	Beckman Coulter	Cat# A63881
Guanidinium thiocyanate	Thermo Fisher	Cat# AM9422
N-Lauroylsarcosine sodium salt solution (Sarkosyl NL)	Sigma	Cat# L7414
Exonuclease l	New England BioLabs	Cat# M0293S
Klenow Fragment	New England BioLabs	Cat# M0212L
Polycarbonate membrane filters 62x22	Fisher Scientific/Sterlitech Corporation	Cat# NC1421644
MACOSKO-2011-10 mRNA Capture Beads	Fisher Scientific/ChemGenes	Cat# NC0927472
Critical commercial assays
Nextera XT DNA Library Preparation Kit	Illumina	Cat# FC-131-1096
Nextseq 500/550 High output v2.5 kit (75 cycles)	Illumina	Cat# 20024906
Kapa HiFi HotStart ReadyMix	Kapa Biosystems	Cat# KK2602
High Sensitivity D5000 ScreenTape	Agilent	Cat# 5067–5592
Qubit dsDNA High-Sensitivity kit	Thermo Fisher	Cat# Q32854
Rneasy Kit	Qiagen, Inc.	Cat# 74004
0.1mm Zirconia/Silica Beads	BioSpec Products	Cat# NC0362415
TaqMan Universal Master Mix II	Life Technologies	Cat# 4440043
Zombie NIR Fixable Viability Kit	BioLegend	Cat# 423105
Deposited data
scRNA-seq data from 10-week p.i. granulomas	This study	Gene Expression Omnibus: GSE200151; https://singlecell.broadinstitute.org/single_cell/study/SCP257
scRNA-seq data from 4-week p.i. granulomas	This study	Gene Expression Omnibus: GSE200151; https://singlecell.broadinstitute.org/single_cell/study/SCP1749
Experimental models: Organisms/strains
Cynomolgus macaques	Valley Biosystems	N/A
Oligonucleotides
Seq-Well ISPCR: AAG CAG TGG TAT CAA CGC AGA GT	Integrated DNA Technologies	N/A
Custom Read 1 Primer: GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C	Integrated DNA Technologies	N/A
Seq-Well TSO: AAG CAG TGG TAT CAA CGC AGA GTG AAT rGrGrG	Integrated DNA Technologies	N/A
Seq-Well Custom P5-SMART PCR hybrid oligo: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACG CCT GTC CGC GGA AGC AGT GGT ATC AAC GCA GAG TAC	Integrated DNA Technologies	N/A
Seq-Well dN-SMRT oligo: AAG CAG TGG TAT CAA CGC AGA GTG ANN NGG NNN B	Integrated DNA Technologies	N/A
Software and algorithms
R project for statistical computing v4.1.2	R Core Team	https://www.r-project.org
R package – Seurat v4.0.2	GitHub	https://github.com/satijalab/seurat
R package – Circlize v0.4.8	CRAN	https://cran.r-project.org/web/packages/circlize/index.html
R package – data.table v1.12.0	GitHub	https://github.com/Rdatatable/data.table
R package – ggplot2 v3.2.1	CRAN	https://cran.r-project.org/web/packages/ggplot2/index.html
R package – ComplexHeatmap v2.7.3	Bioconductor	https://bioconductor.org/packages/ComplexHeatmap/
R package – dplyr v1.0.7	CRAN	https://cran.r-project.org/web/packages/dplyr/
GraphPad Prism v8 (GraphPad software, San Diego, CA), JMP Pro v12	Prism	https://www.graphpad.com/
JMP Pro v12	JMP	https://www.jmp.com/
FlowJo	FlowJo	https://www.flowjo.com/
DropSeqTools v1.12	Macosko et al., 2015	https://github.com/broadinstitute/Drop-seq
OsiriX DICOM	Pixmeo SARL	https://www.oxirix-viewer.com
NIS-Elements AR	Nikon	https://www.microscope.healthcare.nikon.com/products/software/nis-elements/nis-elements-advanced-research
SpectroFlo	Cytek	https://cytekbio.com/pages/spectro-flo