NBDC Research ID: hum0397.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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000680 |
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】 SNP array (genotyping data for 49 participants) |
Controlled-access (Type I) | 2024/04/01 |
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Data Summary
Dataset ID: JGAD000812 (30.1 MB)
Restrictions on data use: NBDC policy
| List of Data Items | document_sukoyaka.tar.gz |
| Participants | 50 healthy individuals (2020) |
| Test items | year, age, sex, region, with/without discontinuation |
| File Name | summer/winter: research.txt (4 KB / 4 KB) |
| 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 (19 KB / 19 KB) |
| 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) |
| 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) |
| 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 |
| 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 (4 KB / 4 KB) |
| 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 (52 KB / 49 KB) |
| Description File | document_sukoyaka.tar.gz |
| Type of Data | Participants | File Name |
|---|---|---|
|
Abundance data of KEGG Orthology for short-read shotgun metagenomic sequencing data of feces |
50 healthy individuals (2020) | metagenomics/summary_functional_ko_abundances_Kyoto.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_Kyoto.tsv (1,700 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_Kyoto.tsv (375 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_Kyoto.tsv (81 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_Kyoto.tsv (12 KB)
|
| Description File | - | document_sukoyaka.tar.gz |
| 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（45 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（244 KB） |
| Description File | document_sukoyaka.tar.gz |
MOLECULAR DATA
| Participants/Materials | 49 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 | JGAD000813 |
| Total Data Volume | 30.1 MB (ped + map) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Nobuya Inagaki
Affiliation: Department of Diabetes, Endocrinology and Nutrition, Kyoto University Graduate School of Medicine
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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data 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 | JGAD000812 | 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 | JGAD000812, JGAD000813 |
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 | JGAD000812, JGAD000813 |
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 | JGAD000812, JGAD000813 |
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. | JGAD000812, JGAD000813 |
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 | JGAD000812, JGAD000813 |
2024/12/10-2028/03/31 |
