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Dataset ID

NHA000193

Type of data
eQTL/pQTL summary statistics for COVID-19
Access criteria
Unrestricted-access
Total data volume
1.7 GB
File formats
  • TXT
  • ZIP
Research
hum0343
Date published
2024-06-21
Date modified
2024-06-21
Secondary ID
hum0343.v3.qtl.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0343.v3.qtl.v1.zip1.7 GB
readme_wang_qs_et_al_2024_japan_covid19_taskforce.txtDictionary file for NHA000193 and E-GEAD-7592.2 KB

Analysis method

eQTL/pQTL summary statistics

Materials and participants
COVID-19 (ICD-10: U071): 1,405 cases (severe cases: 995, mild case: 410)
eQTL analysis: 1,019 cases
pQTL analysis: 1,384 cases
(998 intersecting cases)
  • Health status
    Affected
  • Subject count
    1405 (Individual)
Disease
COVID-19 (U071)
Sample description
read count data of RNA-seq, SNP array data of GWAS and Protein expression data
Experimental method
eQTL
pQTL
Platform
Illumina Infinium Asian Screening Array
Illumina NovaSeq 6000
Olink Explore 3072
QC and filtering
Following GTEx pipeline (https://github.com/broadinstitute/gtex-pipeline/)
Analysis method
Gene level quantification and normalization: RSEM (v1.3.0)
Intron cluster quantification: OlinkAnalyze v3.4.1
The eQTL effects of cis variants (<+-1Mb window of transcription start sites, minor allele count >2) were tested using fastQTL. Then, variant-gene pairs with p-value<0.05 or posterior inclusion probability (PIP) >0.001, annotated with allele frequency (AF), p-value, effect size (beta) and, PIPs were summarized as separate files.
The pQTL effects of cis variants (<+-1Mb window of transcription start sites, minor allele count >2) were tested using fastQTL. Then, variant-gene pairs with p-value<0.05 or posterior inclusion probability (PIP) >0.001, annotated with allele frequency (AF), p-value, effect size (beta) and, PIPs were summarized as separate files.
Processed data type
eQTL summary statistics
pQTL summary statistics
Data use policy
NBDC data sharing policy (JGAP000001)