How to do eQTL analysis?

21 August 2023 1 2K Report

Hello

I am doing an eQTL study and here are the details for that.

I have two mouse strains at two different time points. I already have extracted the RNA fro my tissue of interest and got done with RNAseq (from Novogene) so as to get the Allele Specific Expression (ASE) data.

For eQTL I guess I would need the genotyping data also/GWAS data, so that integration of the ASE and GWAS data can be done for the eQTL analysis.

I am confused from where I can get the genotyping data/GWAS data of the mouse?

Thanks

Frances Lee

Hi, glad to answer your queastion!

Here are some reliable and comprehensive sources of genotyping databases.

Mouse Phenome Database: This open-source resource offers an extensive collection of mouse genetic data, making it an invaluable tool for researchers focusing on murine models. The database includes data from multiple strains of mice, providing a broad spectrum of genetic diversity.

GWAS Central: GWAS Central is a vital platform for anyone conducting genetic association studies. It provides access to summary-level findings from numerous studies worldwide, aiding researchers in identifying potential genetic associations with various traits and diseases.

Mouse Genomes Project: An initiative by the Wellcome Trust Sanger Institute, the Mouse Genomes Project provides high-quality genome sequences of different laboratory mouse strains. This resource aids in the identification of variants, copy number changes, and structural variants.

MGI-Mouse Genome Informatics: As a comprehensive resource, MGI offers integrated data on genetics, genomics, and biology, thus proving invaluable for researchers studying gene functionality and disease associations in mice.

International Mouse Phenotyping Consortium (IMPC): IMPC, with its large-scale phenotyping repository, furnishes abundant data about gene function in mice, thus aiding researchers to correlate genotypes with observable phenotypes.

Shiwali Goyal

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