REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
FITC anti-human CD3 Antibody	Biolegend	Cat#300440; RRID: AB_314060
PerCP anti-human CD45 Antibody	Biolegend	Cat#304026; RRID: AB_893337
PE anti-human CD16 Antibody	Biolegend	Cat#302008; RRID: AB_314207
APC/Cyanine7 anti-human CD14 Antibody	Biolegend	Cat#325620; RRID: AB_830693
Human TruStain FcX™ (Fc Receptor Blocking Solution)	Biolegend	Cat#422302; RRID: AB_2818986
FITC anti-human CD4 Antibody	Biolegend	Cat#357406; RRID: AB_2562357
BV785 anti-human CD8a Antibody	Biolegend	Cat#301046; RRID: AB_11219195
BV650 anti-human CD45RA Antibody	Biolegend	Cat#304136; RRID: AB_2563653
APC/Cyanine7 anti-human CCR7 Antibody	Biolegend	Cat#353212; RRID: AB_10916390
PE/Cyanine7 anti-human CD56 Antibody	Biolegend	Cat#362510; RRID: AB_2563927
PE anti-human CD41 Antibody	Biolegend	Cat#303706; RRID: AB_314376
APC/Cyanine7 anti-human CD235a Antibody	Biolegend	Cat#349116; RRID: AB_2650978
Biological samples
Human Normal Peripheral Blood Mononuclear cells (PBMCs), 20 mil/vial, Frozen	Human Cells Biosciences	Cat#PBMC-C20M
Human Normal Peripheral Blood Mononuclear cells and plasma	Center for Enervating NeuroImmune Disease	Frozen PBMC and plasma
Critical commercial assays
Chromium Single Cell 3ʹ v3	10x Genomics	Cat#CG000183 Rev A and Rev B
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3	10x Genomics	Cat#1000075
Chromium Single Cell B Chip Kit, 16 rxns	10x Genomics	Cat#1000074
Classical Monocyte Isolation Kit, human	Miltenyi Biotech	Cat#130-117-337
CD14 MicroBeads, human	Miltenyi Biotech	Cat#130-050-201
Ultra II Directional RNAseq	NEB	Cat#E7760
CD3 Microbeads, human	Miltenyi Biotech	Cat#130-097-043
Deposited data
Analyzed single cell and bulk RNA seq data		[GEO SuperSeries Accession]: [GSE214284]
Software and algorithms
Cell Ranger mkfastq v6	10x Genomics	RRID:SCR_017344
R package	https://www.R-project.org	RRID:SCR_001905
Seurat v4.1.023	https://doi.org/10.1016/j.cell.2021.04.048	RRID:SCR_016341
prcomp	https://doi.org/10.1038/s41592-019-0619-0	RRID:SCR_014676
DoubletFinder v2.0.380	https://doi.org/10.1016/j.cels.2019.03.003	RRID:SCR_018771
DEseq2 (v2.03)81	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8	RRID:SCR_015687
DESeq2 (v1.34.0)81	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8	RRID:SCR_015687
clusterProfiler (v3.18.1)82	https://doi.org/10.1089/omi.2011.0118	RRID:SCR_016884
fgsea (v.1.20.0)83	https://doi.org/10.1101/060012	RRID:SCR_020938
Singscore (v1.20.0)84	https://bioconductor.org/packages/release/bioc/html/singscore.html	N/A
ggpubr (v0.4.0)	https://rpkgs.datanovia.com/ggpubr/	N/A
CellChat v1.1.361	https://doi.org/10.1016/j.celrep.2022.111155	RRID:SCR_021946
CellChatDB62	https://doi.org/10.1038/s41467-021-21246-9	RRID:SCR_021946
MSigDB database (v7.5.1)30	https://www.gsea-msigdb.org/gsea/msigdb/index.jsp)	RRID:SCR_016863
XGBoost (Python, v0.90)	https://doi.org/10.1145/2939672.2939785	RRID:SCR_021361
FlowJo	BD Bioscience	RRID:SCR_008520
Cutadapt85	https://doi.org/10.14806/ej.17.1.200	RRID:SCR_011841
STAR (v2.7)	dx.doi.org/10.17504/protocols.io.3byl4bjr2vo5/v1	RRID:SCR_004463
ANOVA		RRID:SCR_002427
Proteome Discoverer (PD) 2.5	https://doi.org/10.3390/proteomes9010015	RRID:SCR_014477
Other
RPMI Medium 1640	ThermoFisher	Cat#11875093
Fetal Bovine Serum	ThermoFisher	Cat#10437028
Phosphate Buffered Saline 1x	ThermoFisher	Cat#10010023
DMSO	Sigma Aldrich	Cat#D8418
Histopaque 1077	Sigma Aldrich	Cat#10771
SepMate Tubes	Stemcell Technologies	Cat#85450