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. 2024 Oct 15;27(12):111128. doi: 10.1016/j.isci.2024.111128
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

anti-rhesus IgG1 (clone 7H11) Nonhuman primate reagent resource RRID: AB_2819312
anti-rhesus IgA (clone 9B9) Nonhuman primate reagent resource RRID: AB_2819305
anti-rhesus IgM (clone 2C11-1-5) Life Diagnostics Cat# 2C11-1-5
PE anti-mouse IgG ThermoFisher Cat# 31861; RRID: AB_429715
anti-human CD66b-Pacific Blue BioLegend Cat# 305112; RRID: AB_2563293
PE-Cy5 antihuman CD107a BD Cat# 555802; RRID: AB_396136
PE-Cy7 anti-human CD56 BD Cat# 557747; RRID: AB_396853
APC-Cy7 anti-human CD16 BD Cat# 557758; RRID: AB_396864
Alexa Fluor 700 anti-human CD3 BD Cat# 557943; RRID: AB_396952
PE anti-human MIP-1β BD Cat# 550078; RRID: AB_393549
BV605 anti-human TNF-α BioLegend Cat# 502936; RRID: AB_2563884
FITC anti-human IFN-γ BD Cat# 340449; RRID: AB_400425

Bacterial and virus strains

BCG SSI (Danish strain 1331) Aeras (IAVI) Lot# 050613MF
Mtb Erdman barcode library BEI Resources Cat# NR-50781

Biological samples

Rhesus macaque plasma and BAL (Darrah et al.6) N/A

Chemicals, peptides, and recombinant proteins

LAM BEI Resources Cat# NR-14848
PPD Statens Serum Institute Batch RT50
PstS1 BEI Resources Cat# NR-14859
Apa BEI Resources Cat# NR-14862
HspX BEI Resources Cat# NR-14860
Ag85A BEI Resources Cat# NR-53525
Ag85B BEI Resources Cat# NR-53526
Mpt64 BEI Resources Cat# NR-49435
GroES BEI Resources Cat# NR-14861
Zaire ebolavirus glycoprotein R&D Systems Cat# 9016-EB
GolgiStop BD Cat# 554724
C1Q Sigma Cat# C1740
Sulfo-NHS-LC-LC Biotin ThermoFisher Cat# A35358
Hydrazide biotin ThermoFisher Cat# 21339
FITC-conjugated neutravidin beads ThermoFisher Cat# F8776

Deposited data

Data and metadata This study Data and metadata associated with this study at FAIRDOMHub: https://fairdomhub.org/studies/1198
Custom code This study Scripts to reproduce the computational analysis at Zenodo: https://doi.org/10.5281/zenodo.13880858.29

Experimental models: Cell lines

THP-1 ATCC Cat# TIB202

Software and algorithms

R – pROC package (version 1.18.0) (Robin et al.30) https://cran.r-project.org/web/packages/pROC/pROC.pdf
R – glmnet package (version 3.0-2) (Friedman et al.31) https://cran.r-project.org/web/packages/glmnet/index.html
R – mixOmics package (version 6.10.9) (Rohart et al.32) https://bioconductor.org/packages/release/bioc/html/mixOmics.html
Python – NetworkX library (version 3.9.12) NetworkX https://networkx.org/documentation/stable/install.html
R – lme4 package (version 1.1-31) CRAN https://cran.r-project.org/web/packages/lme4/index.html

Other

FlexMap 3D Luminex N/A
BD LSR II BD N/A