NBDC Research ID: hum0404.v1
SUMMARY
Aims: In this study, we analyze the genomic information of samples from patients with various cardiovascular diseases, including severe heart failure, and identify genetic mutations and polymorphisms that are thought to be related to the pathology of cardiovascular diseases. The purpose is to elucidate the underlying mechanism and develop new therapeutic interventions. The source of the genome to be analyzed is mainly peripheral blood, but in some cases, the genome extracted from the myocardial tissue obtained by myocardial biopsy or iPS cells generated from the patient is also used. In the analysis using iPS cells, we repair genetic mutation using genome editing technology such as CRISPR/Cas9 and analyze the pathological phenotypes.
Methods:
[scRNA-seq] GFP (Control) or S-RBD-sfGFP was added to iPS cell-derived cardiomyocytes and after 48 hours the cells were collected and single-cell RNA sequence analysis was performed.
[WGS] Genomic DNA was extracted from the peripheral blood cells of cardiomyopathy cases and performed whole genome sequencing analysis.
Participants/Materials: iPS cell-derived cardiomyocytes established from a cardiomyopathy case, peripheral blood cells of 3 cardiomyopathy cases
URL: http://www.cardiology.med.osaka-u.ac.jp/?page_id=34330
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000620 | NGS (scRNA-seq) | Controlled-access (Type I) | 2025/09/30 |
| E-GEAD-628 | NGS (scRNA-seq) | Unrestricted-access | 2025/09/30 |
|
JGAS000704 JGAS000705 JGAS000706 |
NGS (WGS) | Controlled-access (Type I) | 2025/09/30 |
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MOLECULAR DATA
| Participants/Materials |
cardiomyopathy (ICD10: I42.0): 1 case GFP or S-RBD-sfGFP was added to iPS cell-derived cardiomyocytes generated from a cardiomyopathy case: 2 samples |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | RNAs extracted from iPS cell-derived cardiomyocytes |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell 3' Reagent Kits v3.1 |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Mapping Methods | Cell Ranger v7.0.1 |
| Reference Genome Sequence | refdata-cellranger-GRCh38-3.0.0 |
| Detecting method for read count (software) | Cell Ranger v7.0.1 |
| QC Methods |
Unique Molecular Identifiers (UMI): 10–17 (Log2) UMIs per Barcode. Thresholds for genes expressed: more than seven (Log2) genes per barcode. Thresholds for mitochondrial UMI: Remove the barcodes with more than 20% of mitochondrial UMI counts. |
| Gene Number |
GFP: 23,234 S-RBD-sfGFP: 23,349 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000749 |
| Genomic Expression Archive ID | E-GEAD-628 |
| Total Data Volume |
JGAD000749: 66.7 GB (fastq) E-GEAD-628: 133 MB (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
cardiomyopathy (ICD10: I42.0): 3 cases hypertrophic cardiomyopathy (HCM): 1 case arrhythmogenic right ventricular cardiomyopathy (ARVC): 1 case myotonic dystrophy: 1 case |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from peripheral blood |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
HCM: JGAD000837 ARVC: JGAD000838 myotonic dystrophy: JGAD000839 |
| Total Data Volume |
JGAD000837: 62.8 GB (fastq) JGAD000838: 64.3 GB (fastq) JGAD000839: 67.5 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shuichiro Higo
Affiliation: Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | SARS-CoV-2 spike receptor-binding domain is internalized and promotes protein ISGylation in human induced pluripotent stem cell-derived cardiomyocytes | doi: 10.1038/s41598-023-48084-7 | E-GEAD-628 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
