Aims: To elucidate the regulation of gene expression in each immune cell subset and its contribution to autoimmune diseases.

Methods: JGAS000220 (JGAD000309, JGAD000310): Various immune cell subsets from 21 systemic sclerosis patients, 26 ANCA associated vasculitis, and 28 healthy controls were collected (Naive_B, SM_B, USM_B, DN_B, Plasmablast, Th1, Th2, Th17, Tfh, Naive_CD4, Mem_CD4, Fr._II_eTreg, Naive_CD8, Mem_CD8, mDC, pDC, CD16p_Mono, CD16n_Mono, NK, Neu) and total RNAs were extracted from each subset. RNA-seq was performed for each sample. E-GEAD-397 / E-GEAD-398 / E-GEAD-420: Whole blood and 28 immune cell subsets from study population were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, LDG, Neu). Whole genome sequencing was performed with whole blood samples. RNA-seq was performed with each immune cell subset samples. After filtering and normalization of the gene expression data, eQTL analysis was performed in each immune cell type. JGAS000296: 24 peripheral blood immune cell subsets from 50 systemic sclerosis patients and 48 healthy controls were collected (Naive_CD4, Mem_CD4, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Th1, Th2, Th17, Tfh, NK, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono, Int_Mono, NC_Mono, mDC, pDC). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered. JGAS000220 (JGAD000371, JGAD000372, JGAD000373): 19 immune cell subsets from study population were collected (Naive_CD4, Mem_CD4, Fr._II_eTreg, Th1, Th2, Th17, Tfh, NK, Naive_CD8, Mem_CD8, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CD16n_Mono, CD16p_Mono, mDC, pDC). RNA-seq was performed with each immune cell subset sample. ATAC-seq of 15 immune cell subsets was also performed. JGAS000486: Various peripheral blood immune cell subsets from 89 healthy volunteers and 136 systemic lupus erhythematosus (SLE) donors were collected (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, EM_CD8, CM_CD8, TEMRA_CD8, NK, Naive_B, USM_B, SM_B, DN_B, Plasmablast, CL_Mono (or CD16n_Mono), CD16p_Mono, Int_Mono, NC_Mono, mDC, pDC, Neu, LDG). 22 SLE patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered. JGAS000598: Various peripheral blood immune cell subsets from 39 healthy volunteers and 50 rheumatoid (RA) donors were collected (CD16p_Mono, CL_Mono, DN_B, Fr_II_eTreg, mDC, Mem_CD4, Naive_B, Naive_CD4, Neu, NK, pDC, Plasmablast, SM_B, Tfh, Th1, Th17, Th2, USM_B). 15 RA patients were analyzed longitudinally. RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered. JGAS000485: Peripheral blood B cell subsets from study population were collected (Naive_B, USM_B, SM_B, DN_B, Plasmablast). RNA-seq was performed with each B cell subset samples. B cell receptor sequences were aligned. JGAS000626: 9 immune cell subsets from study population were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered. JGAS000627: 27 immune cell subsets from study population were collected (Naive_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, ThA, Naive_CD8, Naive_B, SM_B, USM_B, DN_B, Plasmablast, NK, CD16p_Mono, CL_Mono, Neu, mDC, pDC, TEMRA_CD8, CM_CD8, EM_CD8, NC_Mono, Int_Mono, LDG). RNA-seq was performed with each immune cell subset samples. After gene expression quantification samples were filtered. JGAS000648: Peripheral blood, muscle tissue, and bronchial lavage fluid were collected from each subject. For peripheral blood, CD4T cells were collected and scRNA-seq was performed to quantify gene expression. For muscle tissue and bronchial lavage fluid, CD45-positive cells were collected, scRNA-seq was performed, gene expression was quantified, and CD4T cluster was selected. JGAS000762: Peripheral blood T cell subsets from study population were collected (Naive_CD4, Mem_CD4, Th1, Th2, Th17, Tfh, Fr._I_nTreg, Fr._II_eTreg, Fr._III_T, Naive_CD8, TEMRA_CD8, CM_CD8, EM_CD8). RNA-seq was performed with each T cell subset samples. T cell receptor sequences were aligned.

Targets: Systemic Sclerosis, Systemic Lupus Erythematosus, Myositis, Mixed Connective Tissue Disease, Sjögren's Syndrome, Rheumatoid Arthritis, Behçet's Disease, Adult Onset Still's Disease, ANCA-associated Vasculitis, Takayasu's Arteritis, healthy individuals