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

Juan Francisco

Early Stage Researcher

Wilfried Haerty

Main Supervisor

University of East Anglia

PhD enrolment

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.

Early Stage Researcher

Juan Francisco Cervilla

Earlham Institute,

I completed my Bachelor’s degree in Biotechnology at University of Almería (Spain) in 2020. During my last year of Bachelor’s degree, I had the opportunity to participate in two international exchanges, each lasting five months: one at Chonnam National University (South Korea) and the other at Edgewood College (United States). After completing my Bachelor’s degree, I pursued a Master’s degree in Molecular biology applied to Biotechnology business at University of Granada (Spain) in 2021, followed by a Master’s degree in Omics data analysis and Systems biology at the University of Seville (Spain) in 2022.

Throughout years, I gained expertise in a wide range of wet and dry lab skills, both within academia and the industry, ranging from biotechnological applications for agriculture to computational analysis of human samples. Driven by my passion for bioinformatics, omics science and genomics, I aspired to delve deeper into the latest advancements in these fields, particularly long-read sequencing, and single-cell technologies. LongTREC aligns perfectly with my scientific interests and, in conjunction with my project at the Earlham Institute (UK), it will provide me with the tools and knowledge necessary to address my own research inquires and establish a robust network of skilled scientists.

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