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Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

E-GEAD-398

Type of data
Conditional eQTL summary data (significant associations)
Access criteria
Unrestricted-access
Total data volume
565 MB
File formats
  • TXT
  • TAR
Research
hum0214
Date published
2021-04-30
Date modified
2021-04-30
DDBJ Search
E-GEAD-398 (opens in a new tab)

Analysis method

Single-cell eQTL (scRNA-seq + WGS)

Materials and participants
Systemic Lupus Erythematosus (ICD10: M329): 62 cases
Myositis (ICD10: M339, M332): 65 cases
Systemic Sclerosis (ICD10: M340): 67 cases
Mixed Connective Tissue Disease (ICD10: M351): 19 cases
Sjögren's Syndrome (ICD10: M350): 18 cases
Rheumatoid Arthritis (ICD10: M0690): 24 cases
Behçet's Disease (ICD10: M352): 23 cases
Adult Onset Still's Disease (ICD10: M0610): 18 cases
ANCA-associated Vasculitis (ICD10: M318: 25 cases
Takayasu's Arteritis (ICD10: M314): 16 cases
79 healthy controls
  • Health status
    Mixed
  • Subject count
    416 (Individual)
Disease
  • Systemic Lupus Erythematosus
  • Myositis
  • Systemic Sclerosis
  • Mixed Connective Tissue Disease
  • Sjögren's Syndrome
  • Rheumatoid Arthritis
  • Behçet's Disease
  • Adult Onset Still's Disease
  • ANCA-associated Vasculitis
  • Takayasu's Arteritis
Sample description
DNAs extracted from whole blood
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
eQTL
Target
N/A
Reagent kit
TruSeq DNA PCR-Free Library Prep Kit
Fragmentation
TruSeq DNA PCR-Free Library prep kit
Platform
Illumina HiSeq X
Read type
Paired-end
Read length
151 bp
Reference genome
GRCh38
Mapping
BWA-MEM(GRCh38)
QC and filtering
WGS data processing was performed based on the standardized best-practice method proposed by GATK (v 4.0.6.0). Samples with genotyping call rates < 99% were removed. We used BEAGLE (v 5.1) to impute missing genotypes. Variants with call rate < 85%, HWE P-value < 1.0 x 10-6 or minor allele frequency < 1% were excluded.
Analysis method
Genes expressed at low levels (< 5 count in more than 80% samples or < 0.5 CPM in more than 80% samples) were filtered out in each cell subset. The residual autosomal expression data were normalized between samples with TMM, converted to CPM and then normalized across samples using an inverse normal transform. A Probabilistic Estimation of Expression Residuals (PEER) method was applied to normalized expression data to infer hidden covariates. The top 2 genetic principal components, sample collection phase, clinical diagnosis, sex and latent factors were utilized as covariates for eQTL analysis. Mem CD8s, which were collected in Phase1 and divided into CM CD8 and EM CD8 in Phase2, were analyzed jointly with EM CD8 for eQTL analysis because the majority of the Mem CD8 population consisted of EM CD8. For each cell subset conditional eQTL analysis, we used a QTLtools permutation pass with 10,000 permutations to obtain gene-level nominal P value thresholds corresponding to FDR < 0.05. We subsequently performed forward-backward stepwise regression eQTL analysis with a QTLtools conditional pass. For nominal eQTL analysis, we used a QTLtools nominal pass and tested for the association of the variants located within 1Mbp from the TSS of the genes.
Gene count
19,441
Processed data type
eQTL summary statistics
Data use policy
NBDC data sharing policy (JGAP000001)