NBDC Research ID: hum0396.v1

 

SUMMARY

Aims: Investigation of the relationship between the genetic background, gut microbiome, diet, and lifestyle in healthy Japanese.

Methods: Cohort survey and genotyping by SNP array

Participants/Materials: 50 participants (age 20-80)

URL: https://www.naro.go.jp/laboratory/brain/english/sip/sip2/index.html

Dataset IDType of DataCriteriaRelease Date
JGAS000679

Cohort survey for 50 participants (2020)

【Attributes】【Blood test】【Urinalysis】

【Body measurement】【Questionnaire】【Interview】

【Sleep diary】【Heart rate/brain wave during sleep】

【Microbiome composition】【Nutrient intake】

【Food frequency questionnaire】【Metabolomics】

SNP array (genotyping data for 45 participants)

 Controlled-access (Type I) 2024/04/01

*Release Note  

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

 

Data Summary

Cohort survey

Dataset ID: JGAD000810 (32.7 MB)

Restrictions on data use: NBDC policy

 
List of Data Items document_sukoyaka.tar.gz

 

【Attributes】
Participants 50 healthy individuals (2020)
Test items year, age, sex, region, with/without discontinuation
File Name summer/winter: research.txt (3 KB / 3 KB)

 

【Blood test】
Participants 50 healthy individuals (2020)
Test items

【Hematological】White blood cell count (×103/μl), Red blood cell count (×104/μl), Hemoglobin (g/dl), Hematocrit (％), Platelet count (×104/μl)

【Liver-related】GOT (IU/l), GPT (IU/l), γ-GTP (IU/l), ALP (IU/l), LDH (IU/l)

【Kidney-related】BUN (mg/dl), Serum creatinine (mg/dl), Uric acid (mg/dl)

【Blood lipids】Total cholesterol (mg/dl), Triglyceride (mg/dl), HDL cholesterol(mg/dl), LDL cholesterol (mg/dl)

【Blood sugar】Blood sugar (mg/dl), HbA1c (％: NGSP value)

【Hormone】Thyroid stimulating hormone (μIU/ml)

【Other chemical】Total protein (g/dl), Albumin (g/dl), Coline esterase (U/l), Sodium (mEq/l), Chlorine (mEq/l), Magnesium (mg/dl), Calcium (mg/dl), Iron (μg/dl)
File Name summer/winter: blood_test.txt (18 KB / 18 KB)

 

【Urinalysis】
Participants 50 healthy individuals (2020)
Test items Glucose, Protein, Urobilinogen, Bilirubin, Ketone, pH, Occult blood, Serotonin metabolites (5-HIAA: mg/l)
File Name summer/winter: urinalysis.txt (4 KB / 4 KB)

 

【Body measurement】
Participants 50 healthy individuals (2020)
Test items Blood pressure (systolic and diastolic: mmHg), Heart rate (bpm), Height (cm), Waist circumference (cm), Weight (kg), BMI（kg/m2), Body fat percentage (％)
File Name summer/winter: physical_vital.txt (5 KB / 5 KB)

 

【Questionnaire】
Participants 50 healthy individuals (2020)
Test items

questionnaire for education, occupation, family structure, past medical history, history of the present illness, stress/sleep, etc.

questionnaire for the use of antibiotics, characteristics of feces
File Name

summer/winter: questionnaire.txt (95 KB / 80 KB)

summer/questionnaire_antibiotic.csv (5 KB)
Description File document_sukoyaka.tar.gz

 

【Interview】
Participants 50 healthy individuals (2020)
Test items meal time before the examination, with/without blood donation, with/without pregnancy/breastfeeding
File Name summer/winter: interview.txt (3 KB / 3 KB)

 

【Sleep diary】
Participants 50 healthy individuals (2020)
Test items questionnaire for physical condition before sleep, awakenings, physical condition after awakening, etc.
File Name summer/winter: diary_calc.txt (78 KB / 76 KB)

 

【Heart rate/brain wave during sleep】
Participants 50 healthy individuals (2020)
Test items Heart rate and brain wave data during sleep (90 items includes sleep duration, number of awakenings, average heart rate)
File Name SIP2B観察研究（心拍と脳波）_2020_summer/winter.csv (50 KB / 50 KB)
Description File document_sukoyaka.tar.gz

 

【Microbiome composition】
Type of DataParticipantsFile Name

Abundance data of KEGG Orthology

for short-read shotgun metagenomic sequencing data of feces

 50 healthy individuals (2020) metagenomics/summary_functional_ko_abundances_Miyazaki.tsv (2,900 KB)

Species-level abundance data computed by Kraken2

for short-read shotgun metagenomic sequencing data of feces

 50 healthy individuals (2020) metataxonomics/summary_taxonomic_species_abundances_Miyazaki.tsv (1,800 KB)

Genus-level abundance data computed by Kraken2

for short-read shotgun metagenomic sequencing data of feces

 50 healthy individuals (2020) metataxonomics/summary_taxonomic_genus_abundances_Miyazaki.tsv (386 KB)

Family-level abundance data computed by Kraken2

for short-read shotgun metagenomic sequencing data of feces

 50 healthy individuals (2020) metataxonomics/summary_taxonomic_family_abundances_Miyazaki.tsv (83 KB)

Phylum-level abundance data computed by Kraken2

for short-read shotgun metagenomic sequencing data of feces

 50 healthy individuals (2020) metataxonomics/summary_taxonomic_phylum_abundances_Miyazaki.tsv (12 KB)

 
Description File - document_sukoyaka.tar.gz

 

【Nutrient intake】
Participants 50 healthy individuals (2020)
Test items Intakes of 57 nutrients includes total protein and sodium, and intakes of 148 food groups includes rice and bean curd
File Name

栄養素摂取量_食品群別摂取量/SIP2020夏_栄養素摂取量_食品群別摂取量.txt（45 KB）

栄養素摂取量_食品群別摂取量/SIP2020冬_栄養素摂取量_食品群別摂取量.txt（46 KB）
Description File document_sukoyaka.tar.gz

 

【Food frequency questionnaire】
Participants 50 healthy individuals (2020)
Test items 705-item food frequency questionnaire includes beef and octopus, etc
File Name 2020_winter/ffq_all.txt（300 KB）
Description File

 

【Metabolomics】
Type of DataParticipantsFile Name
Targeted metabolomics data for hydrophilic metabolites in blood plasma 50 healthy individuals (2020)

metabolomics/summary_targeted_blood_datasets_Miyazaki.tsv（286 KB）
Targeted metabolomics data for hydrophilic metabolites in feces 50 healthy individuals (2020)

metabolomics/summary_targeted_feces_datasets_Miyazaki.tsv（238 KB）
Non-targeted metabolomics data for hydrophilic metabolites in feces 50 healthy individuals (2020)

metabolomics/summary_untargeted_datasets_Miyazaki.tsv（3,200 KB）
Targeted metabolomics data for bileacids in feces 50 healthy individuals (2020)

metabolomics/summary_bileacids_datasets_Miyazaki.tsv（9 KB）
Non-targeted metabolomics data for lipids in feces 50 healthy individuals (2020)

metabolomics/summary_lipids_datasets_Miyazaki.tsv（144 KB）
Non-targeted metabolomics data for proteins in blood plasma 50 healthy individuals (2020)

metabolomics/summary_olink_datasets_Miyazaki.tsv（77 KB）
Description File - document_sukoyaka.tar.gz

 

MOLECULAR DATA

SNP array
Participants/Materials 45 healthy individuals
Targets genome wide SNPs
Target Loci for Capture Methods -
Platform Affymetrix [Japonica Array v2]
Source DNAs extracted from peripheral blood cells
Cell Lines -
Reagents (Kit, Version) Axiom 2.0 Reagent Kit
Genotype Call Methods (software) Axiom Analysis suite v4.0.0.28
Filtering Sample QC: Dish QC ≥0.82 & QC call rate ≥97%
Marker Number (after QC) 659,709 SNPs
Japanese Genotype-phenotype Archive Dataset ID JGAD000811
Total Data Volume 32.7 MB (ped + map)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Jun Nishihira

Affiliation: Department of Medical Management and Informatics, Hokkaido Information University

URL: https://www.naro.go.jp/laboratory/brain/english/sip/sip2/index.html

Project / Group Name: Cross-ministerial Strategic Innovation Promotion Program(SIP)　Technologies for smart bio-industry and agriculture "Contribution to healthy longevity based on the health system through food"

Funds / Grants (Research Project Number):

NameTitleProject Number
Cross-ministerial Strategic Innovation Promotion Program (SIP)　Technologies for smart bio-industry and agriculture Contribution to healthy longevity based on the health system through food -

 

PUBLICATIONS

TitleDOIDataset ID
1
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Kenta Fujiwara R&D Laboratories, Self-Medication, Taisho Pharmaceutica Japan Investigation of Health Conditions Using SIP Observational Study Data JGAD000810 2024/03/29-2025/03/31
Yuki Kawaharada Tech & Biz Development Div., Chitose Laboratory Corporation Japan Integrated Data Analysis and Demonstration of Data Integration Using Datasets from Comprehensive Observational Studies Conducted by Multiple Institutions JGAD000810,
JGAD000811		 2024/07/11-2028/03/31
Kazuhiro Miyaji Health Care & Nutritional Science Institute, Morinaga Milk Japan Cross-sectional study of the relationship between health status, nutritional status, and lifestyle habits such as diet, sleep, and stress status in Japanese adults JGAD000810,
JGAD000811		 2024/07/11-2028/03/31
Mamoru Kimura R&D Division, Kewpie Corporation Japan Integrated Data Analysis and Demonstration of Data Integration Using Datasets from Comprehensive Observational Studies Conducted by Multiple Institutions JGAD000810,
JGAD000811		 2024/10/15-2028/03/31
Tomohiko Nishijima Mechanism-based Research Laboratory, Ezaki Glico Co., Ltd. Japan Development of integrated data analysis and data linkage techniques using data from multi-institutional exhaustive research study trials. JGAD000810,
JGAD000811		 2024/10/22-2028/03/31
Mitsue Nishiyama Tsumura Advanced Technology Research Laboratories, Tsumura & Co. Japan Integrated Data Analysis and Demonstration of Data Integration Using Datasets from Comprehensive Observational Studies Conducted by Multiple Institutions JGAD000810,
JGAD000811		 2024/12/10-2028/03/31