NBDC Research ID: hum0393.v2
SUMMARY
Aims: To explore new biomarkers or therapeutic target molecules using samples from patients with autoimmune diseases
Methods:
JGAS000693: CD4+CD45RA-CD25hiCD127lo Treg cells were sorted on Moflo XDP cell sorter (Beckman Coulter) from each peripheral blood sample. Total RNA was extracted with TRIZOL-LS (ThermoFisher/Invitrogen) for RNA-seq.
JGAS000630: CD19+cells were separated by magnetic-activated cell sorting (MACS) using human CD19 MicroBeads (Miltenyi Biotec), and then PanT cells were also sorted using human PanT Cell Isolation Kit (Miltenyi Biotec) from each sample. Total RNA was extracted with TRIZOL-LS (ThermoFisher/Invitrogen) for RNA-seq.
Participants/Materials:
JGAS000693: Twelve peripheral blood samples were collected from six treatment-naïve rheumatoid arthritis (RA) patients and six healthy individuals.
JGAS000630: Submandibular glands (SMGs) (N=3) and peripheral blood mononuclear cells (PBMCs) (N=4) were collected from four patients with treatment naïve IgG4 related diseases (IgG4-RD). PBMCs were also collected from three patients with primary Sjögren's syndrome (pSS) who fulfilled American College of Rheumatology (ACR)/European League Against Rheumatism (EULAR) Classification Criteria for pSS, and three healthy controls.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000693 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/08/23 |
| JGAS000630 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/10/28 |
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MOLECULAR DATA
RNA-seq (JGAS000693 / JGAS000630)
| Participants/Materials |
[JGAS000693] treatment-naïve rheumatoid arthritis (ICD10: M690): 6 cases (6 samples) 6 healthy individuals (6 samples) [JGAS000630] treatment naïve IgG4-RD (ICD10: C359): 4 cases Submandibular glands: 3 samples PBMCs: 4 samples primary Sjögren's syndrome (ICD10: C350): 3 cases PBMCs: 3 samples Healthy control: 3 individuals PBMCs: 3 samples CD19+cells and PanT cells were obtained from each sample: total 26 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500] |
| Library Source |
JGAS000693: RNAs extracted from CD4+CD45RA-CD25hiCD127lo Treg cells sorted on a cell sorter from each peripheral blood sample JGAS000630: RNAs extracted from CD19+cells and PanT cells |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II DNA Library Prep Kit, takara smarter kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 36 bp x 2 |
| Mapping Methods | CLC Genomics Workbench |
| Reference Genome Sequence | hg19 |
| Detecting method for read count (software) | CLC Genomics Workbench |
| QC | - |
| Gene Number | 57,768 |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000826: rheumatoid arthritis, healthy individuals JGAD000760: IgG4-RD, primary Sjögren's syndrome, healthy individuals |
| Total Data Volume |
JGAD000826: 5.7 GB (fastq, TPM matrix data: csv) JGAD000760: 26.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroto Tsuboi
Affiliation: Department of Rheumatology, University of Tsukuba
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (B) | Mechanisms and exhaustion of T follicular regulatory cells in rheumatoid arthritis | 21H02959 |
| establishment of university fellowships towards the creation of science technology innovation, JST | Analysis of age-related changes in regulatory T cell function in rheumatoid arthritis | JPMJFS2106 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Gene expression analysis by RNA-Seq and development of novel therapeutic target in IgG4-related disease | 21K08471 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Mechanisms of age-related Treg dysfunction in an arthritic environment | doi: 10.1016/j.clim.2024.110337 | JGAD000826 |
| 2 | Analysis of lymphocytes specific gene expression pattern by RNA-Seq in patients with IgG4-related disease: Comparison between submandibular glands and peripheral blood | doi: 10.1093/mr/roaf059 | JGAD000760 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
