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,

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