Growth Protocol:	-
Treatment Protocol:	-
Extract Protocol:	For all patients and controls, heparin anticoagulated whole-blood was processed within 4 hours of sampling. PBMCs were separated by density gradient centrifugation using Ficoll-Paque Plus medium (GE Healthcare Life science, Little Chalfont, UK) and washed twice, first with cold PBS and then with cold PBS supplemented with 0.5% sterile endotoxin-free bovine serum albumin (Divbio Science Europe, Breda, the Netherlands). PBMC’s were resuspended in PBS containing 0.5% BSA and 2mm EDTA and the concentration PBMCs was determined using a Coulter Counter. PBMCs were resuspended in IMDM medium containing 20% filter-sterilized fetal calf serum and pen/strep, after which an equal part of the same medium containing 20% DMSO was slowly added while continuously stirring and working on ice. 3-5 million PBMCs were viably stored in 1.8 ml cryogenic vials (Corning #430388), which were steadily brought to -80 degrees Celsius. After 24-72 hours, the cells were transferred to liquid nitrogen storage until further analysis. After thawing, all samples averaged 90% viability as determined by FACS analysis. PBMCs were thawed, stained with viability dye and 500,000 cells were sorted using a FACS Sony Sorter selecting alive, singlet cells. The cells were incubated with FC blocker for 10 minutes, after which each sample was incubated with TotalSeq Hashtag antibody tags to enable multiplexing and subsequent deconvoluting. After Hashtag staining the cells were pooled into four pools of five samples, each sample contributing equally to their respective pool. Cells were counted manually by light microscopy and Neubauer chambers. Each pooled sample was then incubated for 30 minutes with our TotalSeq oligo-conjugated antibody panel (see the Key Resources Table) for later surface protein marker quantification.
Library Construction Protocol:	Libraries were generated using the Chromium Single Cell 5′ Library & Gel Bead Kit v1.1 (10X genomics, Pleasanton, CA) following the manufacturer’s instructions. In short, pooled cells were loaded aiming the capture of 10,000 cells per pool. Libraries were generated according to standard protocol (Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 rev E). The amplified mRNA and antibody-derived tags were divided by size and sequenced separately.

Molecule Type:	polyA(+) RNA
Library Source:
Library Layout:	PAIRED
Library Strand:	-
Platform:	ILLUMINA
Instrument Model:	Illumina HiSeq 4000
Strand-Specific:	-

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate