NBDC Research ID: hum0321.v1
SUMMARY
Aims: We analyze thymic epithelial cells and intrathymic immune cells in the normal thymus and in thymoma and thymic hyperplasia tissues, which have been strongly implicated in autoimmune diseases. These analyses include conventional FACS analysis and single-cell analysis. The development, differentiation, and function of immunocompetent cells will also be analyzed from the perspective of gene expression as well as thymic regulation of immune cell responses. The results of this research will enable the identification of key molecules in thymic immune regulation as a pathogenic mechanism in various autoimmune diseases and will serve as a starting point for the development of new drug targets.
Methods: Blood cells and thymus tissues were collected and subjected to single-cell RNA sequencing using a next-generation sequencer.
Participants/Materials: Peripheral blood samples from patients with myasthenia gravis, or thymus glands from the patients resected at the time of surgery were used for the analysis.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000482 | NGS (scRNA-seq) | Controlled-access (Type I) | 2022/06/17 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
myasthenia gravis (ICD10: G70.01): 4 cases peripheral blood: 2 samples, thymoma surgery: 4 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from peripheral blood cells or thymoma surgery samples |
| Cell Lines | - |
| Library Construction (kit name) |
(3' profiling) Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 or Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics) (5'+VDJ profiling) Chromium Next GEM Single Cell 5’ Kit v2 and Chromium Single Cell Human BCR Amplification Kit or Chromium Single Cell Human TCR Amplification Kit (10x Genomics) |
| Fragmentation Methods | manufacturer’s protocol |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000599 |
| Total Data Volume | 235.1 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tatsusada Okuno
Affiliation: Department of Neurology, Osaka University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Specially Promoted Research | Study of the function and development of regulatory T cells | 6H06295/ |
| Innovation and Clinical Research Center Project, Japan Agency for Medical Research and Development (AMED) | Study of Immunoregulatory technology targeting regulatory T cells | JP21gm0010005 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma | doi: 10.1038/s41467-022-31951-8 | JGAD000599 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Yukinori Okada | Department of Statistical Genetics, Osaka University Graduate School of Medicine | Japan | Elucidation of disease etiology by trans-layer omics analysis | JGAD000599 | 2024/03/05-2025/07/14 |
