Accessing Genotyping Data and GWAS Data for eQTL Studies

Genotyping data and Genome-Wide Association Study (GWAS) data are fundamental components in conducting expression Quantitative Trait Loci (eQTL) studies, providing critical insights into the relationship between genetic variations and complex traits. In this tutorial, we will explore reputable databases where researchers can access comprehensive genotypic and phenotypic data for eQTL analyses.

1. Mouse Phenome Database:

• Link: Mouse Phenome Database
• Description: An open-source resource providing extensive mouse genetic data, encompassing multiple strains. Ideal for researchers working with murine models to explore genetic diversity.

2. GWAS Central:

• Link: GWAS Central
• Description: A crucial platform for genetic association studies, offering summary-level findings from various studies globally. Enables researchers to identify potential genetic associations with diverse traits and diseases.

3. Mouse Genomes Project:

• Link: Mouse Genomes Project
• Description: An initiative by the Wellcome Trust Sanger Institute, providing high-quality genome sequences for different laboratory mouse strains. Essential for identifying genetic variants, copy number changes, and structural variants.

4. MGI-Mouse Genome Informatics:

• Link: MGI-Mouse Genome Informatics
• Description: A comprehensive resource offering integrated data on genetics, genomics, and biology. Invaluable for researchers studying gene functionality and disease associations in mice.

5. International Mouse Phenotyping Consortium (IMPC):

• Link: IMPC
• Description: Features a large-scale phenotyping repository, providing abundant data about gene function in mice. Facilitates the correlation of genotypes with observable phenotypes.

Obtaining Data and Incorporating into eQTL Studies:

1. Download Data:
   • Visit the respective databases and follow their data download procedures.
   • Ensure you have sufficient storage space and bandwidth for large datasets.
2. Data Analysis:
   • Utilize the downloaded data in studies of eQTLs.
   • Investigate statistically significant relationships between genetic variants and gene expression levels.
3. Enhance Comprehension:
   • Enrich your understanding of the genetic basis of complex traits using the obtained genotyping and GWAS data.