M2: Bioinformatics of Autism Spectrum Disorders

Title: RNA-seq data integration in autism spectrum disorders of the TSZH3 knock-out mouse

The Tshz3 gene codes for a zinc finger transcription factor (TSHZ3) involved in several developmental processes in the ureter, the central nervous system and skeletal muscle. Due to the function of Tshz3 in brain development, the loss of Tshz3 leads to death at birth, as animals fail to breathe (Caubit, et al., 2010). Postnatal loss of Tshz3, on the other hand, leads to autism-like behaviors (Chabbert, et al., 2019), as well as kidney failure. We have generated transcriptomic data from Tshz3 knock-out tissues of brain and kidney. The aim of this M2 project is to analyze and integrate these data with each other, as well as publicly available data on renal tumors, as well as neurological disorders. To this end, the student will make use of a platform we have generated for data integration with a large set of publicly available data and adapt it to Tshz3 data (mitoXplorer (Yim et al., in revision (NAR); http://mitoxplorer.ibdm.univ-mrs.fr/).

This project is a joint project between the Habermann lab and the Fasano lab at the IBDM.

Required skills: NGS data analysis ; RNA-seq data analysis ; data integration of transcriptomic data; data curation of ASD genes; programming in python, JavaScript and R ; scripting in bash/shell commands ; communication skills (written/spoken) in English.

Ideal starting date: January/February 2020

Interested? Send your CV, letter of motivation and contact information of referees to bianca.habermann [at ] univ-amu.fr.