NBDC Research ID: hum0492.v1
SUMMARY
Aims: Although advances in our understanding of the disease mechanisms and the development of new drugs has improved the prognosis for patients with immune-inflammatory diseases such as rheumatoid arthritis, inflammatory bowel disease and autoimmune liver disease, there are still some patients who do not respond well to treatment or who are unable to discontinue the use of steroid drugs. This study aims to identify biomarkers, such as genes and proteins, that can be also used as new therapeutic targets in the blood and tissues of patients with these immune-inflammatory diseases who are starting new treatment.
Methods: Single cell RNA sequencing/TCR/BCR repertoire analyses, Spatial transcriptome analysis (Visium)
Participants/Materials: labial salivary glands from 28 patients with Sjögren's syndrome and 10 patients with Sicca
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000773 | Controlled-access (Type I) | 2025/08/12 |
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MOLECULAR DATA
| Participants/Materials |
Sjögren's syndrome (ICD10: M350): 19 cases Sicca: 8 cases labial salivary glands: total 27 samples (6 patients with Sjögren's syndrome and 3 patients with Sicca are also used in Visium analysis) |
| Targets | scRNA-seq/TCR/BCR repertoire |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X] |
| Library Source | RNAs extracted from T cell or B cell obtained from labial salivary glands |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Cell Ranger (version 5.0.1) |
| Reference Genome Sequence | GRCh38 |
| Detecting method for read count (software) | Cell Ranger (version 5.0.1) |
| Gene number | 1478 on average |
| Repertoire analysis Methods (software) | Cell Ranger (version 5.0.1) |
| QC | Cell Ranger (version 5.0.1) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000915 |
| Total Data Volume | 1.24 TB (bam, csv) |
| Comments (Policies) | NBDC policy |
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
Sjögren's syndrome (ICD10: M350): 15 cases Sicca: 5 cases labial salivary glands: total 20 samples (6 patients with Sjögren's syndrome and 3 patients with Sicca are also used in scRNA-seq/TCR/BCR repertoire analysis) |
| Targets | Visium Spatial Gene Expression, Histological image |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400] |
| Library Source | labial salivary glands |
| Cell Lines | - |
| Library Construction (kit name) | Visium CytAssist Spatial Gene Expression for FFPE |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1: 28 bp, read2: 50 bp |
| Software | spaceranger-2.0.1 |
| Reference | GRCh38 |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000915 |
| Total Data Volume | 1.24 TB (fastq, jpg/tiff) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masaru Takeshita
Affiliation: Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine
Project / Group Name: -
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Single cell integrated analysis of antigen specificity and gene expression for the cure of autoimmune diseases | 20K17430 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of the Mechanisms of Autoantibody Production at Lesion Sites in Autoimmune Diseases | 22K08528 |
| KAKENHI Grant-in-Aid for JSPS Fellows | Elucidation of Sjögren's syndrome pathogenesis through retrotransposon sequences | 21J00596 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | Molecular signatures in pre-RA patients by multi-omics analysis | 20H03720 |
| Keio University Academic Promotion Fund | Elucidation of Autoimmune Mechanisms at Lesion Sites in Autoimmune Diseases and Development of Antigen-Specific Immunosuppressive Therapies | - |
| Keio University Fukuzawa Memorial Fund | Comprehensive Understanding of Autoimmunity and Practical Application of Antigen-Specific Immunosuppressive Therapies | - |
| Keio University Next-Generation Research Promotion Program | Comprehensive Analysis of Salivary Gland Lesions as Sites of Autoimmune Responses | - |
| Mochida Memorial Foundation for Medical and Pharmaceutical Research — Research Grant — | lucidation of Autoimmune Mechanisms in Lesional Tissues of Sjögren’s Syndrome and Development of Antigen-Specific Immunosuppressive Therapies | - |
| Kowa Life Science Foundation — Research Grant — | Elucidation of Molecular Mechanisms Involved in Autoimmune Responses at Lesion Sites in Sjögren’s Syndrome | - |
| Takeda Science Foundation — Medical Research Grant — | Elucidation of Autoimmune Mechanisms at Lesion Sites in Autoimmune Diseases | - |
| Japan Rheumatism Foundation — Research Grant for Rheumatic Disease Investigation — | Elucidation of Molecular Mechanisms Involved in Autoantigen-Specific B Cell Immune Responses in Various Autoimmune Diseases and Identification of Therapeutic Targets | - |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
