NBDC Research ID: hum0113.v3
SUMMARY
Aims: Identification of RNA biomarkers in Parkinson's disease (PD) patients
Methods: Transcriptome sequencing (CAGE-seq)
Participants/Materials: Whole blood samples from 39 PD patients and 20 non-PD (healthy) controls
iPS-derived neuron cells provided by 2 PD patients with PARK2 mutations and 3 non-PD (healthy) controls
iPS-derived neuronal stem cells (NSC) provided by 2 PD patients with PARK2 mutations and 3 non-PD (healthy) controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000119 | NGS (CAGE-seq) | Controlled-access (Type I) | 2020/04/24 |
| JGAS000142 | NGS (CAGE-seq) | Controlled-access (Type I) | 2021/07/30 |
| JGAS000318 | NGS (CAGE-seq) | Controlled-access (Type I) | 2022/07/29 |
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MOLECULAR DATA
JGAS000119 / JGAS000142 / JGAS000318
| Participants/Materials |
PD patients (ICD10: G20) and non-PD (healthy) controls - Whole blood: 39 PD patients and 20 non-PD controls - iPS-derived neurons and NSCs: 2 PD patients (3 samples) with PARK2 mutations and 3 non-PD controls |
| Targets | CAGE-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNA extracted from whole blood, iPS-derived neurons, and iPS-derived NSCs |
| Cell Lines | - |
| Library Construction (kit name) | nAnT-iCAGE protocol (PMID: 24927836) |
| Fragmentation Methods | - |
| Spot Type |
whole blood, iPS-derived neurons and NSCs (JGAD000129 and JGAD000211): Single-end iPS-derived neurons and NSCs (JGAD000429): Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 47-50 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000129: whole blood JGAD000211: iPS-derived neurons and NSCs JGAD000429: iPS-derived neurons and NSCs |
| Total Data Volume |
JGAD000129: 35 GB (fastq) JGAD000211: 88 GB (fastq) JGAD000429: 32 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Piero Carninci
Affiliation: RIKEN Center for Integrative Medicine Science, Division of Genomic Medicine
Project / Group Name:-
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) | Development of metabolite biomarker specific for Parkinson's disease and identification of drug seeds based on its molecular target | JP19gm0710011 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson’s Disease | doi: 10.1038/s41597-019-0022-9 | JGAD000129 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
