NBDC Research ID: hum0440.v1
SUMMARY
Aims: The primary causes of neurodegenerative diseases, as well as peripheral nerve disorders like autoimmune encephalitis and chronic inflammatory demyelinating polyneuropathy, remain unclear. Although numerous therapeutic drugs have been developed for the conditions at hand, it is known that even within the same neurological and muscular diseases, there are differences in clinical progression and initial symptoms among individual patients. We aim to identify proteins related to this clinical progression and develop treatment strategies tailored to the pathology.
Methods: 10x Visium FFPE with CytAssist
Participants/Materials: Thymoma, Thymic hyperplasia
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000672 | NGS (Visium Spatial Gene Expression), Histological image | Controlled-access (Type I) | 2024/05/17 |
| E-GEAD-747 | NGS (Visium Spatial Gene Expression), Histological image | Unrestricted-access | 2024/05/17 |
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MOLECULAR DATA
Visium Spatial Gene Expression, Histological image
| Participants/Materials |
Thymoma (ICD10: C37): 7 cases, including 2 cases complicating myasthenia gravis (ICD10: G700) tumor tissue: 8 samples (For one duplicate thymoma, sampling was performed at two locations from the same tissue.) Thymic hyperplasia (ICD10: E32.0): 2 cases complicating myasthenia gravis (ICD10: G700) thymic hyperplasia: 2 samples |
| Targets | Visium Spatial Gene Expression |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400RS] |
| Library Source | RNAs extracted from tumor tissues or thymic hyperplasia samples |
| Cell Lines | - |
| Library Construction (kit name) | Visium Spatial Gene Expression Slide and Reagent Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | R1:28bp, R2:100bp |
| Software | Space Ranger v2.0.1 |
| Reference | GRCh38-2020-A |
| Tissue Image | hematoxylin-eosin staining |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000802 |
| Genomic Expression Archive ID | E-GEAD-747 |
| Total Data Volume |
JGAD000802: 244.2 GB (fastq) E-GEAD-747: 1.2 GB (tif, png, csv, json) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Tatsusada Okuno
Affiliation: Department of Neurology, Osaka University Graduate School of Medicine
Project / Group Name: Elucidation of proteins associated with the clinical course of refractory neuromuscular diseases using nerve and muscle tissue
URL: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Grants-in-Aid for Scientific Research Grant (B) | Trial to elucidate of the pathogenesis of autoimmune neuromuscular diseases and catalogue their treatment | 23H02826 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Spatial transcriptomics elucidates medulla niche supporting germinal center response in myasthenia gravis thymoma | doi: 10.1101/2024.02.05.579042 | JGAD000802 E-GEAD-747 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
