NBDC Research ID: hum0290.v1
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SUMMARY
Aims: Through genome cohort studies targeting healthy volunteers who work or live in the Kashiwa-no-ha area, we aim to realize a safer and more comfortable living environment and build a foundation for drug discovery research and the development of personalized medicine.
Methods: WGS, 10x scRNA, 10x TCR, 10x BCR, CyTOF analyses were performed using blood samples collected from healthy volunteers aged 18 years or older who worked or lived in the Kashiwa-no-ha area.
Participants/Materials: 7 healthy volunteers aged 18 years or older who worked or lived in the Kashiwa-no-ha area
URL： https://kero.hgc.jp/longread_viewer/single_cell/open/
https://kero.hgc.jp/longread_viewer/single_cell/open/data/Expression/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000321 | Controlled-access (Type I) | 2022/03/07 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials | 2 healthy volunteers (2 samples) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform |
Illumina [NovaSeq 6000] Nanopore [PromethION] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) |
Illumina: TruSeq DNA Nano kit Nanopore: SQK-LSK109 Kit |
| Fragmentation Methods |
Illumina: Ultrasonic fragmentation (Covaris) Nanopore: - |
| Spot Type |
Illumina: Paired-end Nanopore: Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
Illumina: 300 bp Nanopore: - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000432 |
| Total Data Volume | 2.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 7 healthy volunteers (57 samples) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | 10x Genomics [Chromium Controller] |
| Library Source | RNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000432 |
| Total Data Volume | 2.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 7 healthy volunteers (57 samples) |
| Targets | TCR-seq |
| Target Loci for Capture Methods | - |
| Platform | 10x Genomics [Chromium Controller] |
| Library Source | RNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000432 |
| Total Data Volume | 2.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 7 healthy volunteers (35 samples) |
| Targets | BCR-seq |
| Target Loci for Capture Methods | - |
| Platform | 10x Genomics [Chromium Controller] |
| Library Source | RNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000432 |
| Total Data Volume | 2.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 6 healthy volunteers (30 samples) |
| Targets | CyTOF@ Mass cytometry |
| Target Loci for Capture Methods | 30 proteins related to immune response |
| Platform | Helios a CyTOF system [Fluidigm] |
| Source | peripheral blood cells |
| Cell Lines | - |
| Reagents | Maxper Direct Immune Profiling Assay, 30 Marker - 25 test (Cat. #201325) |
| Parameter | 30 |
| Acquire/analyze data software | Maxpar Pathsetter (Cat. #401018) |
| Experiment date | 2020/11/1 - 2021/7/31 |
| Experiment variables | individual variation, timepoint post-vaccination, vaccination type (influenza, SARS-CoV-2) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000432 |
| Total Data Volume | 2.2 TB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Yutaka Suzuki
Affiliation: Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo
Project / Group Name: -
URL： -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| JST Moonshot R&D – MILLENNIA Program | Understanding and Control of Virus-Human Interaction Networks | JPMJMS2025 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Intensive Single Cell Analysis Reveals Immune Cell Diversity among Healthy Individuals | doi: 10.26508/lsa.202201398 | JGAD000432 |
| 2 | Multimodal single-cell analyses of peripheral blood mononuclear cells of COVID-19 patients in Japan | doi: 10.1038/s41598-023-28696-9 | JGAD000432 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
