NBDC Research ID: hum0099.v1
SUMMARY
Aims: Expression quantitative trait loci analysis using human immune cells
Methods: Total RNA from whole blood cells and five immune cell populations (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes) and genomic DNA isolated from whole blood cells were used for RNA-seq and genotyping, respectively.
Participants/Materials: 105 Japanese healthy volunteers
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000085 |
RNA-seq (Fragments Per Kilobase of exon per Million mapped fragments: FPKM) |
Controlled-access (Type I) | 2017/04/24 |
| hum0099.v1.eqtl.v1 |
eQTL (Summary of stats for each variant [ex. effect size, P-value]) |
Unrestricted-access | 2017/04/24 |
*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 |
105 healthy volunteers (21 males, 84 females) Five immune cell populations (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes) and whole blood cells (6 samples each) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | total RNAs extracted from five immune cell populations (CD4+ T cells, CD8+ T cells, B cells, NK cells, and monocytes) and whole blood cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kits |
| Fragmentation Methods | heat denaturation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 125 bp |
| QC | Total read counts < 2 x 107 、Mapping rates < 90%、Mean inter-sample correlation coefficients < 0.94 |
| Mapping Methods | Tophat2 |
| Reference Genome Sequence | GRCh37 |
| Detecting Methods for Variation | Cufflinks + Gencode version 19 gene model (in FPKM unit) |
| Total Reads / Uniquely Mapped Reads | 4.52 x 107 / 4.39 x 107 on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000085 |
| Total Data Volume | 53 MB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 105 healthy volunteers (21 males, 84 females) |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium OmniExpressExome BeadChips] |
| Library Source | gDNA extracted from whole blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Infinium OmniExpressExome BeadChips kit |
| Genotype Call Methods (softwares) | GenCall software (GenomeStudio) |
| Imputation Methods | IMPUTE2 + 1000 Genomes Phase 1 v3 |
| Filtering Methods | MAF ≥ 0.05, average maximum posterior probability ≥ 0.9, INFO ≥ 0.4 (5,600,101 variants) |
| Marker Numbers (after QC) | 563,436 SNPs (reference sequence: hg19) |
| NBDC Dataset ID | hum0099.v1.eqtl.v1 |
| Total Data Volume | 1778.8 MB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigators (Affiliation):
Kazuhiko Yamamoto (The University of Tokyo, Graduate School of Medicine, Allergy and Rheumatology)
Michiaki Kubo (RIKEN Center for Integrative Medical Science)
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Collaboration with Takeda Pharmaceutical Company Limited. | Identification of treatment targets based on eQTL |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis | doi:10.1038/ng.3885 |
JGAD000085 hum0099.v1.eqtl.v1 |
USERS (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Kyuyoung Song | University of Ulsan college of medicine | JGAD000085 | 2018/08/06-2019/06/05 | ||
| Tatsuhiko Tsunoda | Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University | Research on big data analysis for precision medicine | JGAD000085 | 2018/12/18-2021/06/19 | |
| Tatsuhiko Tsunoda | Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University | Research on sequence, image data analysis for precision medicine | JGAD000085 | 2019/06/06-2023/08/31 | |
| Yuta Kochi | Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University | Japan | Genetic study of complex diseases through comprehensive analysis of functional genetic variations | JGAD000085 | 2023/04/10-2024/03/31 |
