Research Project 1
Alternative splicing regulation at the single cell resolution: Protocols and computational developments for long read RNA-Seq in single cell
About the Project
Earlham Institute
Norwich, UK
Wilfried Haerty
Main Supervisor
University of East Anglia
PhD enrolment
Yearly salary
47.259,87 € (Gross)
Research Objectives
The low error rate of PacBio LRS makes it suitable for the study of the immune repertoire (T-cell and B-cell receptors) at single cells and to characterize the effect of chromosome duplications on gene expression. New library preparation methods are required to increase sequencing throughput. Our objectives are:
- Develop an optimized concatenation protocol for low input material to optimize quantification of PacBio lrRNA-seq data.
- Develop a method for identifying and quantifying transcripts resulting from recombination such as VDJ events.
- Develop a method to quantify transcript expression under different ploidy levels.
Envisioned Secondments
- Uppsala University (SciLifeLab), Adam Ameur: learn protocols for low-input material library preparation.
- Biobam (Stefan Goetz): Learn & apply transcript-specific functional analysis tools.
About the Main Supervisor and Host Group
Wilfried Haerty
Earlham Institute,
UK
As Group Leader of Evolutionary Genomics, my current research interests focus on characterising functional non-coding sequences and the evolutionary constraints acting on these elements across many species with a strong focus on mammalian genomes. Another significant part of my research involves the identification and characterisation of functional long non-coding RNAs in humans. I use comparative genomics approaches to quantify the action of selection acting on non-coding elements, with a strong focus on the patterns of sequence variation among populations