NBDC Research ID: hum0395.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: 963 participants
URL: https://www.naro.go.jp/laboratory/brain/english/sip/sip2/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000678 |
Cohort survey for 【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 962 participants) |
Controlled-access (Type I) | 2024/04/01 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
Data Summary
Dataset ID: JGAD000808 (492.0 MB)
Restrictions on data use: NBDC policy
| List of Data Items | document_sukoyaka.tar.gz |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer/winter) |
| Test items | year, age, sex, region, with/without discontinuation |
| File Name |
summer/winter: research.txt (39 KB / 37 KB) 2020_summer/winter: research.txt (20 KB / 19 KB) |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 307 healthy individuals (2020 winter) |
| 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 (126 KB / 116 KB) 2020_summer/winter: blood_test.txt (69 KB / 65 KB) |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 307 healthy individuals (2020 winter) |
| Test items | Glucose, Protein, Urobilinogen, Bilirubin, Ketone, pH, Occult blood, Serotonin metabolites (5-HIAA: mg/l) |
| File Name |
summer/winter: urinalysis.txt (49 KB / 47 KB) 2020_summer/winter: urinalysis.txt (25 KB / 24 KB) |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 307 healthy individuals (2020 winter) |
| 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 (60 KB / 56 KB) 2020_summer/winter: physical_vital.txt (30 KB / 28 KB) |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 307 healthy individuals (2020 winter) |
| Test items |
summer: 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 winter: history of the present illness, questionnaire for stress/sleep, etc. |
| File Name |
summer/winter: questionnaire.txt (796 KB / 581 KB) 2019_summer: questionaire_antibiotics_2019.csv (72 KB) 2020_summer/winter: questionnaire.txt (420 KB / 310 KB) questionaire_antibiotic_2020.csv (29 KB) |
| Description File | document_sukoyaka.tar.gz |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 307 healthy individuals (2020 winter) |
| Test items | meal time before the examination, with/without blood donation, with/without pregnancy/breastfeeding |
| File Name |
summer/winter: interview.txt (42 KB / 38 KB) 2020_summer/winter: interview.txt (20 KB / 19 KB) |
| Participants |
642 healthy individuals (2019 summer/winter) 321 healthy individuals (2020 summer), 306 healthy individuals (2020 winter) |
| Test items | questionnaire for physical condition before sleep, awakenings, physical condition after awakening, etc. |
| File Name |
summer/winter: diary_calc.txt (805 KB / 805 KB) 2020_summer/winter: diary_calc.txt (450 KB / 428 KB) |
【Heart rate/brain wave during sleep】
| Participants |
625 healthy individuals (2019 summer), 575 healthy individuals (2019 winter) 319 healthy individuals (2020 summer), 308 healthy individuals (2020 winter) |
| Test items | Heart rate and brain wave data during sleep (90 items includes sleep duration, number of awakenings, average heart rate) |
| File Name |
2019_summer_vital.tar.gz/2019_winter_vital.tar.gz (808 KB / 1700 KB) 2020_summer_vital.tar.gz/2020_winter_vital.tar.gz (420 KB / 881 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 |
641 healthy individuals (2019 summer) 158 healthy individuals (2019 winter) 309 healthy individuals (2020 summer/winter) |
summary_functional_ko_abundances_20192020_Hokkaido.tsv (61800 KB) |
|
Species-level abundance data computed by Kraken2 for short-read shotgun metagenomic sequencing data of feces |
641 healthy individuals (2019 summer) 158 healthy individuals (2019 winter) 309 healthy individuals (2020 summer/winter) |
summary_taxonomic_species_abundances_20192020_Hokkaido.tsv (30300 KB) |
|
Genus-level abundance data computed by Kraken2 for short-read shotgun metagenomic sequencing data of feces |
641 healthy individuals (2019 summer) 158 healthy individuals (2019 winter) 309 healthy individuals (2020 summer/winter) |
summary_taxonomic_genus_abundances_20192020_Hokkaido.tsv (7700 KB) |
|
Family-level abundance data computed by Kraken2 for short-read shotgun metagenomic sequencing data of feces |
641 healthy individuals (2019 summer) 158 healthy individuals (2019 winter) 309 healthy individuals (2020 summer/winter) |
summary_taxonomic_family_abundances_20192020_Hokkaido.tsv (1700 KB) |
|
Phylum-level abundance data computed by Kraken2 for short-read shotgun metagenomic sequencing data of feces |
641 healthy individuals (2019 summer) 158 healthy individuals (2019 winter) 309 healthy individuals (2020 summer/winter) |
summary_taxonomic_phylum_abundances_20192020_Hokkaido.tsv (246 KB) |
| Description File | - | document_sukoyaka.tar.gz |
| Participants |
625 healthy individuals (2019 summer), 579 healthy individuals (2019 winter) 316 healthy individuals (2020 summer), 303 healthy individuals (2020 winter) |
| Test items | Intakes of 57 nutrients includes total protein and sodium, and intakes of 148 food groups includes rice and bean curd |
| File Name |
2019_summer_vital.tar.gz/2019_winter_vital.tar.gz (808 KB / 1700 KB) 2020_summer_vital.tar.gz/2020_winter_vital.tar.gz (420 KB / 881 KB) |
| Description File |
document_sukoyaka.tar.gz |
【Food frequency questionnaire】
| Participants |
609 healthy individuals (2019 winter) 307 healthy individuals (2020 winter) |
| Test items | 705-item food frequency questionnaire includes beef and octopus, etc |
| File Name |
2019_winter/ffq_all.txt (2,900 KB) 2020_winter/ffq_all.txt (1,500 KB) |
| Description File | document_sukoyaka.tar.gz |
| Type of Data | Participants | File Name |
|---|---|---|
| Targeted metabolomics data for hydrophilic metabolites in blood plasma |
160 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
floraindex_blood_2019_winter.txt (359 KB) metabolomics/summary_targeted_blood_datasets2020_Hokkaido.tsv (248 KB) |
| Targeted metabolomics data for hydrophilic metabolites in feces |
158 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
floraindex_feces_2019_winter.txt (274 KB) metabolomics/summary_targeted_feces_datasets2020_Hokkaido.tsv (207 KB) |
| Non-targeted metabolomics data for hydrophilic metabolites in feces |
158 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
floraindex_feces_nontarget_2019_winter.txt (1,500 KB) metabolomics/summary_untargeted_dataset2020_Hokkaido.tsv (2,900 KB) |
| Targeted metabolomics data for bileacids in feces |
158 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
kazusa_feces_2019_winter.txt (27 KB) metabolomics/summary_bileacids_dataset2020_Hokkaido.tsv (8 KB) |
| Non-targeted metabolomics data for lipids in feces |
158 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
kazusa_feces_nontarget_2019_winter.tsv (382 KB) metabolomics/summary_lipids_dataset2020_Hokkaido.tsv (128 KB) |
| Non-targeted metabolomics data for proteins in blood plasma |
160 healthy individuals (2019 winter) 43 healthy individuals (2020 summer) |
olink_blood_2019_winter.tsv (241 KB) metabolomics/summary_olink_datasets2020_Hokkaido.tsv (67 KB) |
| Description File | - | document_sukoyaka.tar.gz |
MOLECULAR DATA
| Participants/Materials | 962 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 | JGAD000809 |
| Total Data Volume | 492.0 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):
| 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 |
|---|---|---|---|---|---|
