NBDC Research ID: hum0290.v2
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, scATAC-seq, Olink, and methylation array 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 | |
| JGAS000637 | Controlled-access (Type I) | 2025/06/06 | |
| E-GEAD-1053 | NGS (scRNA-seq, scATAC-seq) | Unrestricted-access | 2025/06/06 |
| E-GEAD-1058 | CyTOF | Unrestricted-access | 2025/06/06 |
| E-GEAD-1059 | Olink | Unrestricted-access | 2025/06/06 |
| E-GEAD-1060 | Methylation array | Unrestricted-access | 2025/06/06 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. 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 | Fluidigm [Helios, a CyTOF System] |
| 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 |
| Participants/Materials | 51 healthy volunteers (51 samples) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-T7] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | MagAttract HMW DNA Kit, 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 | JGAD000767 |
| Total Data Volume | 12.876 TB (fastq) |
| Comments (Policies) | NBDC policy |
scRNA-seq, scATAC-seq (JGAS000637 / E-GEAD-1053)
| Participants/Materials | 94 healthy volunteers (125 samples) |
| Targets | scRNA-seq, scATAC-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/X] |
| Library Source | DNAs/RNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Chromium Next GEM Single Cell Multiome ATAC + Gene Expression |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) |
scRNA-seq: 118bp scATAC-seq: 99bp |
| Software | CellRanger-arc (ver2.0.0) |
| Reference Genome Sequence | refdata-GRCh38-1.0.0. |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000767 |
| Genomic Expression Archive ID | E-GEAD-1053 |
| Total Data Volume |
JGAD000767：12.876 TB (fastq) E-GEAD-1053：300 GB (txt, tsv) |
| Comments (Policies) | NBDC policy |
CyTOF (JGAS000637 / E-GEAD-1058)
| Participants/Materials | 43 healthy volunteers (43 samples) |
| Targets | CyTOF@ Mass cytometry |
| Target Loci for Capture Methods | 30 proteins related to immune response |
| Platform | Fluidigm [Helios, a CyTOF System] |
| 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) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000767 |
| Genomic Expression Archive ID | E-GEAD-1058 |
| Total Data Volume |
JGAD000767: 12.876 TB (txt) E-GEAD-1058: 300 GB (txt) |
| Comments (Policies) | NBDC policy |
Olink (JGAS000637 / E-GEAD-1059)
| Participants/Materials | 35 healthy volunteers (35 samples) |
| Targets | Protein expression (batch1: 2941 proteins, batch2: 2939 proteins) |
| Target Loci for Capture Methods | - |
| Platform | Olink [Olink Explore 3072] |
| Library Source | Plasma |
| Cell Lines | - |
| Library Construction (kit name) | Olink Explore 3072 |
| Fragmentation Methods | - |
| Spot Type | - |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | - |
| Detecting Methods for Proteins (software) | NPX manager |
| Normalization Methods | NPX manager |
| Validation Methods | NPX manager |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000767 |
| Genomic Expression Archive ID | E-GEAD-1059 |
| Total Data Volume |
JGAD000767: 12.876 TB (txt, csv) E-GEAD-1059: 300 GB (txt, csv) |
| Comments (Policies) | NBDC policy |
Methylation array (JGAS000637 / E-GEAD-1060)
| Participants/Materials | 51 healthy volunteers (88 samples) |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium MethylationEPIC BeadChip] |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | EZ DNA Methylation™ Kit, Infinium® Human Methylation 450K BeadChip kit |
| Algorithms for Calculating Methylation-rate (software) | iScan system, GenomeStudio Software |
| Filtering Methods | - |
| Normalization of microarray | - |
| Probe Number | 865,918 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000767 |
| Genomic Expression Archive ID | E-GEAD-1060 |
| Total Data Volume |
JGAD000767: 12.876 TB (txt) E-GEAD-1060: 300 GB (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 |
| 3 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
