Uncovering the dark transcriptome and proteome with long-read sequencing

Overview

Parts of the transcriptome and proteome are invisible to current technologies. We refer to them as the dark transcriptome and proteome and they encompass uncharacterised mRNA and protein isoforms. Importantly, this hidden molecular phenotype is believed to play a critical role in animal health and behavior.

Recent developments in mRNA analytical methods such as long-read sequencing (PacBio, ONT) have enabled better characterization of isoforms and are redefining the transcriptome landscape in many species. We and others have found that data generated from these cutting-edge sequencing platforms can dramatically improve the interpretation of  RNA-Seq -based quantitative transcriptomics and SWATH-based quantitative proteomics datasets.

Research activities

Utilizing already collected long-read sequencing data, this project will fine-tune the bioinformatics pipelines for the interpretation of RNA-Seq and SWATH datasets. The project will involve R programming and the use of command line tools.

Outcomes

The project will set the foundation for robust and reproducible informatics pipelines and generate isoform-resolved map of transcriptome and proteome in selected animal models of health and behavior.

Skills and experience

Good knowledge of R statistical environment and proficiency in command line.

Scholarships

You may be eligible to apply for a research scholarship.

Explore our research scholarships

Keywords

• proteomics
• transcriptomics
• long-read sequencing
• multi-omics
• bioinformatics

Contact

Contact the supervisor for more information.