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
University of East Anglia
47.259,87 € (Gross)
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.
- 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
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