NBDC Research ID: hum0423.v2
SUMMARY
Aims: To elucidate the pathomechanism of inflammatory muscle diseases using multi-omics analysis
Methods: Short read and long read RNA sequencing, Single nucleus RNA sequencing
Participants/Materials: 22 + 1 sarcoid myopathy patients, 400 muscular disease patients (Controls)
URL: https://mgc.ncnp.go.jp/index_en.php
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000636 | NGS (RNA-seq) | Controlled-access (Type I) | 2024/10/23 |
| JGAS000636 (Data addition) | Controlled-access (Type I) | 2024/12/25 |
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MOLECULAR DATA
| Participants/Materials |
sarcoid myopathy (ICD10: D86.8, G73.7): 22 cases (22 samples) Short read RNA sequencing: 16 cases (16 samples) Long read RNA sequencing: 6 cases (6 samples) Muscular disease (non-sarcoid myopathy): 400 controls (400 samples) Short read RNA sequencing: 400 controls (400 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform |
MGI [DNBSEQ-G400] Nanopore [PromethION] |
| Library Source | RNAs extracted from muscular lesions |
| Cell Lines | - |
| Library Construction (kit name) |
MGI: Not available Nanopore: cDNA-PCR Sequencing Kit (SQK-PCS111) |
| Fragmentation Methods |
MGI: Reverse transcription by random priming Nanopore: - |
| Spot Type |
MGI: Paired-end Nanopore: Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
MGI: 100 bp Nanopore: 918 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000766 |
| Total Data Volume | 523.3 GB + 2.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
sarcoid myopathy (ICD10: D86.8, G73.7): 2 cases (2 samples) 1 case is also used in RNA-seq |
| Targets | snRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNAs extracted from muscular lesions |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000766 |
| Total Data Volume | 2.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Aritoshi Iida
Affiliation: Medical Genome Center, National Center of Neurology and Psychiatry
Project / Group Name: Section of Clinical Genome Analysis, Department of Clinical Genome Analysis
URL: https://mgc.ncnp.go.jp/index_en.php
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Comprehensive elucidation of the pathomechanism of muscle diseases by multi-omics analyses | JP22ek0109490 |
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 |
|---|---|---|---|---|---|
