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

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000085

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])

Un-restricted Access 2017/04/24

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

JGAS00000000085

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 (Illumina)
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
Japan Genotype-Phenotype Archive Data Set ID JGAD00000000085
Total Data Volume 53 MB (txt)
Comments (Policies) NBDC policy

 

 

hum0099.v1.eqtl.v1

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) Illumina Infinium OmniExpressExome BeadChips kit
Genotype Call Methods (softwares) GenCall software(GenomeStudio)
Imputation方法 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 Data Set 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):

NameTitleProject Number
Collaboration with Takeda Pharmaceutical Company Limited. Identification of treatment targets based on eQTL

 

PUBLICATIONS

TitleDOIData Set ID
1 Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis doi:10.1038/ng.3885

JGAD00000000085

hum0099.v1.eqtl.v1

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