REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-CD4_clone-RPA-T4	Biolegend	CAT#300501; LOT#B226034; RRID: AB_314069
anti-CD8_clone-Hit8a	Biolegend	CAT#300901; LOT#B164480; RRID: AB_314105
anti-CD197 (CCR7)_clone-G043H7	Biolegend	CAT#353202; LOT#B199725; RRID: AB_10945157
anti-CD45RA_clone-HI100	Biolegend	CAT#304102; LOT#B198595; RRID: AB_314406
anti-CD45RO_clone-UCHL1	Biolegend	CAT#304202; LOT#B177325; RRID: AB_314418
anti-CD95_clone-DX2	Biolegend	CAT#305602; LOT#B206684; RRID: AB_314540
anti-CD27_clone-O323	Biolegend	CAT#302802; LOT#B186305; RRID: AB_314294
anti-CD28_clone-CD28.2	Biolegend	CAT#302901; LOT#B207053; RRID: AB_314303
anti-CD57_clone-HCD57	Biolegend	CAT#322302; LOT#B206682; RRID: AB_535988
anti-CD38_clone-HIT2	Biolegend	CAT#303502; LOT#B213310; RRID: AB_314354
anti-HLA-DR_clone-L243	Biolegend	CAT#307602; LOT#B217166; RRID: AB_314680
anti-CD49d (α4 integrin)_clone-9F10	Biolegend	CAT#304301; LOT#B185063; RRID: AB_314427
anti-CD29 (β1 integrin)_clone-TS2/16	Biolegend	CAT#303001; LOT#B200527; RRID: AB_314317
anti-CD194 (CCR4)_clone-1G1	BD	CAT#551121; LOT#6355945; RRID: AB_2074502
anti-CD25_clone-BC96	Biolegend	CAT#302602; LOT#B164472; RRID: AB_314272
anti-CD127_clone-A019D5	Biolegend	CAT#351302; LOT#B207381; RRID: AB_10718513
anti-CD183 (CXCR3)_clone-G025H7	Biolegend	CAT#353702; LOT#B218188; RRID: AB_10983073
anti-CD196 (CCR6)_clone-G034E3	Biolegend	CAT#353401; LOT#B148881; RRID: AB_10918626
anti-CCR10_clone-6588-5	Biolegend	CAT#341502; LOT#B199209; RRID: AB_1595419
anti-CXCR5_clone-J252D4	Biolegend	CAT#356901; LOT#B163804; RRID: AB_2561810
anti-TCR Vα24-Jα18_clone-6B11	Biolegend	CAT#342902; LOT#B204558; RRID: AB_2229301
anti-TCR γ/δ_clone-11F2	Nordic MUbio / Biozol	CAT#NMB-MUB1809P; LOT#7104; RRID: n/a
anti-TCR Vα7.2_clone-3C10	Biolegend	CAT#351702; LOT#B209777; RRID: AB_10900258
anti-CD161_clone-DX12	BD	CAT#556079; LOT#B7075709; RRID: AB_396346
anti-NKG2D_clone-1D11	Biolegend	CAT#320802; LOT#B228271; RRID: AB_492956
anti-CD159a (NKG2A)_clone-#131411	R&D	CAT#MAB1059-100; LOT#FVY0318061; RRID: AB_2280982
anti-CD19_clone-HIB19	Biolegend	CAT#302202; LOT#B250155; RRID: AB_314232
anti-IgD_clone-IA6-2	Biolegend	CAT#348202; LOT#B24390; RRID: AB_10550095
anti-CD24_clone-ML5	Biolegend	CAT#311102; LOT#B240399; RRID: AB_314851
anti-CD138_clone-DL-101	Biolegend	CAT#352302; LOT#B258491; RRID: AB_10915555
anti-CD14_clone-M5E2	Biolegend	CAT#301802; LOT#B257124; RRID: AB_314184
anti-CD16_clone-B73.1	Biolegend	CAT#360702; LOT#B243320; RRID: AB_2562693
anti-CD123/IL-3R_clone-6H6	Biolegend	CAT#306002; LOT#B254974; RRID: AB_314576
anti-CD11c_clone-3.9	Biolegend	CAT#301602; LOT#B252725; RRID: AB_314172
anti-CD56_clone-HCD56	Biolegend	CAT#318302; LOT#B254021; RRID: AB_604092
anti-CD279 (PD-1)_clone-EH12.2H7	Biolegend	CAT#329902; LOT#B250570; RRID: AB_940488
anti-CD152 (CTLA-4)_clone-BNI3	Biolegend	CAT#369602; LOT#B224872; RRID: AB_2566610
anti-CD3_clone-37895	Biolegend	CAT#317301; LOT#B201401; RRID: AB_571926
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_01	Biolegend	CAT#394601; LOT# B272595; RRID: AB_2750015
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_02	Biolegend	CAT#394603; LOT# B272602; RRID: AB_2750016
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_03	Biolegend	CAT#394605; LOT# B272598; RRID: AB_2750017
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_04	Biolegend	CAT#394607; LOT# B270523; RRID: AB_2750018
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_05	Biolegend	CAT#394609; LOT# B270803; RRID: AB_2750019
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_06	Biolegend	CAT#394611; LOT# B272604; RRID: AB_2750020
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_07	Biolegend	CAT#394613; LOT# B272606; RRID: AB_2750021
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_08	Biolegend	CAT#394615; LOT# B272605; RRID: AB_2750022
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_09	Biolegend	CAT#394617; LOT# B270545; RRID: AB_2750023
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_10	Biolegend	CAT#394619; LOT# B264719; RRID: AB_2750024
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_12	Biolegend	CAT#394623; LOT# B264718; RRID: AB_2750025
anti-CD298/β2-microglobulin-clone_LNH-94/2M2-hashtag_13	Biolegend	CAT#394625; LOT# B264717; RRID: AB_2750026
Biological samples
Peripheral blood mononuclear cells of MS patients and healthy individuals	Biobank of the Institute of Neuroimmunology and Multiple Sclerosis (INIMS)	https://www.inims.de/#biobanking
Brain tissue of MS patients and control brain tissue	UK Multiple Sclerosis Society Tissue Bank	http://www.imperial.ac.uk/medicine/multiple-sclerosis-and-parkinsons-tissue-bank/
Critical commercial assays
Chromium Single Cell Gene Expression 3′ v2	10X genomics	No longer commercially available
Chromium Single Cell Gene Expression 3′ v3	10X genomics	CAT#1000074, 1000092, 1000213
Library Preparation (LP) glass slides	Spatial Transcriptomics, Stockholm	The company is now part of 10X genomics. The original assay is no longer available (compare 10X Visium product)
Deposited data
ScRNA-seq data of PBMCs from MS patients and healthy individuals	This paper	GEO: GSE144744
Bulk RNA-sequencing data of sorted PBMC populations	Ref18	GEO: GSE107011
Bulk RNA-sequencing data of natalizumab-treated T cells	Ref7	GEO: GSE37783
Sc-RNA-seq data of brain tissue from MS patients and control tissue	Ref17	SRA: PRJNA544731
Oligonucleotides
See Table S4		N/A
Software and algorithms
bcl2fastq_v2.20.0.422	Illumina	https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
zUMIs_v2.5.6b	40	https://github.com/sdparekh/zUMIs
samtools_v1.9	41	https://github.com/samtools/samtools
STAR_v2.6.0c	42	https://github.com/alexdobin/STAR
CITE-seq-Count_v1.4.2	https://doi.org/10.5281/zenodo.2590196	https://github.com/Hoohm/CITE-seq-Count
R_v3.6.1	The R Project for Statistical Computing	https://www.r-project.org/
Seurat_v3.1.1	43	https://satijalab.org/iocon/
DoubletFinder_v2.0.2	44	https://github.com/chris-mcginnis-ucsf/DoubletFinder
sctransform_v0.2.0	45	https://github.com/ChristophH/sctransform
SAVER-X_v1.0.0	46	https://github.com/jingshuw/SAVERX
Flowjo_v10.5.3	BD	https://www.flowjo.com/
DESeq2_v1.22.1	47	http://bioconductor.org/packages/release/bioc/html/DESeq2.html
Tidyverse_v1.2.1.9000	48	https://tidyverse.org
nf-core/rnaseq_v1.4.2	49	https://github.com/nf-core/rnaseq
AUCell_v1.4.1	50	https://bioconductor.org/packages/release/bioc/html/AUCell.html
clusterProfiler_v3.10.1	51	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
Cytoscape_v3.6.1	52	https://cytoscape.org/
ST pipeline_v1.5.1	Spatial Transcriptomics	https://github.com/SpatialTranscriptomicsResearch/st_pipeline