Reagent or resource	Source	Identifier
Antibodies (Clone)
CD3 (UCHT1)	Beckman Coulter	#A66327
CD3 (SK7)	BioLegend	#344804
CD3 (SK7)	BioLegend	#344807
CD4 (13B8.2)	Beckman Coulter	#IM2468
CD4 (SK3)	BioLegend	#344638
CD8 (B9.11)	Beckman Coulter	#A82791
CD8 (SK1)	BioLegend	#344723
CD8 (SK1)	BioLegend	#344730
CD14 (RM052)	Beckman Coulter	#B36297
CD14 (M5E2)	BioLegend	#301804
CD16 (3G8)	Beckman Coulter	#A66330
CD16 (3G8)	BioLegend	#302059
CD19 (J3-119)	Beckman Coulter	#B76283
CD19 (HIB19)	BioLegend	#302205
CD19 (HIB19)	BioLegend	#302226
CD45 (J33)	Beckman Coulter	#B36294
CD56 (N901)	Beckman Coulter	#A21692
CD56 (HCD56)	BioLegend	#318304
CD56 (HCD56)	BioLegend	#318327
CD138 (B-A38)	Beckman Coulter	#A40316
CD138 (DL-101)	BioLegend	#352306
HLA-DR (Immu-357)	Beckman Coulter	#B92438
HLA-DR (L243)	BioLegend	#307610
HLA-DR (L243)	BioLegend	#307629
IgD (IA6- 2)	BioLegend	#348222
CD5 (UCHT2)	BioLegend	#300629
CD11c (Bu15)	BioLegend	#337220
CD20 (2H7)	BioLegend	#302336
CD20 (2H7)	BioLegend	#302347
CD21 (Bu32)	BioLegend	#354922
CD24 (ML5)	BioLegend	#311122
CD25 (BC96)	BioLegend	#302629
CD27 (M-T271)	BioLegend	#356412
CD28 (CD28.2	BioLegend	#302908
CD38 (HB-7)	BioLegend	#356642
CD39 (A1)	BioLegend	#328218
CD40 (5C3)	BioLegend	#334337
CD40 (5C3)	BioLegend	#334322
CD45RA (HI100)	BioLegend	#304134
CD57 (QA17A04)	BioLegend	#393325
CD57 (QA17A04)	BioLegend	#393303
CD80 (2D10)	BioLegend	#305229
CD86 (BU63)	BioLegend	#374206
CD95 (DX2)	BioLegend	#305642
CD117 (104D2)	BioLegend	#313205
CD123 (6H6)	BioLegend	#306019
CD127 (A019D5)	BioLegend	#351333
CD127 (A019D5)	BioLegend	#351336
CD183 (G025H7)	BioLegend	#353704
CD192 (K036C2)	BioLegend	#357213
CD194 (L291H4)	BioLegend	#359419
CD195 (J418F1)	BioLegend	#359118
CD196 (G034E3)	BioLegend	#353417
CD197 (G043H7)	BioLegend	#353214
CD206 (15-2)	BioLegend	#321131
CD294 (BM16)	BioLegend	#350117
CD335 (9E2)	BioLegend	#331907
KLRG1 (14C2A07)	BioLegend	#368607
PD-1 (EH12.2H7)	BioLegend	#329906
Tim-3 (F38-2E2)	BioLegend	#345012
CTLA-4 (BNI3)	BioLegend	#369614
TIGIT (A15153G)	BioLegend	#372711
CCR10 (1B5)	BioLegend	#564771
FoxP3 (PCH101)	eBioscience	#12-4776-42
CX3CR1 (2A9-1)	BioLegend	#341626
Biological samples
Relapsing–remitting multiple sclerosis (RRMS) patients (n = 148)	Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany	NA
Relapsing–remitting multiple sclerosis (RRMS) patients (n = 20)	Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany	NA
Autoimmune limbic encephalitis (ALE) patients (n = 81)	Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany	NA
Primary diffuse large B cell lymphoma of the CNS (CNS-DLBCL) patients (n = 9)	Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany	NA
IDH-wildtype glioma patients (n = 33)	Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany	NA
Glioblastoma patients (n = 18)	Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany	NA
Somatic symptom disorder (SD) patients (n = 110)	Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany	NA
Healthy controls (n = 19)	Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany	NA
Chemicals, peptides, and recombinant proteins
Zombie Aqua™ Fixable Viability Kit	BioLegend	#423102
VersaLyse	Beckman Coulter	#IM3648
Flow count fluorospheres	Beckman Coulter	#7547053
DPBS, no calcium, no magnesium	Thermo Fisher Scientific	#14190094
Fetal Bovine Serum (FBS)	Fisher Scientific	#17593595
SepMate isolation tubes	StemCell Technologies,	#85450
FcR Blocking Reagent	Miltenyi Biotec	#130-059-901
EDTA 0,5 M Ultra Pure	Thermo Fisher Scientific	#15575020
Critical commercial assays
Foxp3/Transcription Factor Staining Buffer Set	eBioscience	#00-5523-00
Deposited data
MFC and clinical data	ABCD-J data catalog	https://data.abcd-j.de/dataset/d55bbe2f-7e97-5e30-a03b-27119dd0c68d/1.0?tab=content
Software and algorithms
Kaluza Flow Cytometry Analysis (v2.1)	Beckman Coulter	https://www.beckman.com/flow-cytometry/software/kaluza
OMIQ	Dotmatics	www.omiq.ai
R studio’ (2023.06.1)	R Core Team	https://www.r-project.org
R ggplot2 (v3.4.4)	Hadley Wickham	https://www.rdocumentation.org/packages/ggplot2
FactorMineR (v2.11)	Francois Husson	https://www.rdocumentation.org/packages/FactoMineR/versions/2.9
R pheatmap (v1.0.12)	Raivo Kolde	https://www.rdocumentation.org/packages/pheatmap/versions/1.0.10/topics/pheatmap
R mixOmics (v6.26.0)	F R, B G, A S, K-A LC (2017). “mixOmics: An R package for 'omics feature selection and multiple data integration.” PLoS computational biology, 13(11), e1005752	http://www.mixOmics.org
BioRender	Shiz Aoki	https://www.biorender.com/
Other
Navios flow cytometer	Beckman Coulter	NA
CytoFLEX-S	Beckman Coulter	NA