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 IDType of DataCriteriaRelease 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

*Release Note

*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationResearch TitleData in Use (Dataset ID)Period of Data Use