Single cell RNA and CITE sequencing of cells from synovial tissue biopsies of healthy donors, and Rheumatoid Arthritis (RA) patients with active disease or sustained clinical remission

The dataset includes the raw FASTQ files generated from the 10x Genomics Single Cell 3' v3.1 experiments. For samples processed with TotalSeq Hashtag reagents, the corresponding hashtag oligonucleotide and condition annotations are provided as separate .csv files. The processed matrices contain filtered readcounts for each cell barcode and, where multiplexing was used, the demultiplexed sample assignments derived from the hashtag data as .csv files. Synovial biopsies were taken using 14G Precisa Needle (HS Hospital Service, Italy) in ultrasound-guided protocol, and digested as described previously (Alivernini et al, 2020). Live CD45+ cells from the synovial tissue (ST) of healthy donors (n=3), patients with active RA (n=5) and patients in sustained remission (n=2) were sorted for single cell RNA (scRNA) or CITE (scCITE) sequencing using the 10x Genomics platform. Maximum 20,000 immune cells from tissue were sorted into Protein LoBind 1.5 ml Eppendorf tube containing 300 µl of RPMI media with 10% of FSC. Cells were loaded onto a Chromium Controller (10X Genomics) for single-cell partitioning, followed by library preparation using Single-Cell 3' Reagent Kits v3.1. For 3 healthy ST and 4 ST from active RA (Figure S1), Totalseq Hashtag were used (Biolegend #394601, #394603, #394605, #394607, #394609) to combine 2 samples per run, and TotalSeq™-A Human Universal Cocktail (V1.0) was used to collect protein expression (CITEseq) data together with transcriptome data. Single-cell libraries were sequenced on the Illumina HiSeq 4000 system to a minimum depth of 50k reads/cell.