LeedsOmics bioinformatics team ran the third “Introduction to RNA-Seq Data Analysis” Workshop in 2019. This two-day training workshop is suitable to anyone who is adopting RNA-Seq strategy in their own research and needs to develop a certain level of confidence on running a full RNA-Seq analysis pipeline on their own, from the quality control of raw reads in the first step up to obtaining the list of differentially expressed genes and visualising results. Like previous editions, this event was a success, with a great feedback from the audience, who now claim to feel confident on executing standalone tools through the Linux command line and/or within the R environment.
On the 7th of October 2019, we organized a “Welcome Back” event mainly directed to current students already part of our LeedsOmics community, as well as fresh ones who will potentially be involved with omics research and, consequently, interested in joining our activities throughout the new academic year. Dr Julie Aspden and Dr Niamh Forde (LeedsOmics co-founders from FBS and FMH, respectively) led a talk about LeedsOmics as a virtual institute, addressing its actions and goals. Dr Dapeng Wang (Senior Bioinformatics Research Officer) and Dr Elton Vasconcelos (Bioinformatics Research Officer) also contributed to the presentation by exhibiting the procedures on recruiting LeedsOmics bioinformatics support, as well as advertising the training workshops and coding club sessions periodically offered to omics researchers at the University of Leeds. The event counted with the attendance of about 50 people, including both students and PIs, who were all able to informally interact with each other through a coffee and cake reception at the end.
I am a postdoctoral researcher in the Glioma Genomics group at Leeds Institute of Medical Research (LIMR). The main focus of my work, which is funded by The Brain Tumour Charity, is to understand how glioblastoma (GBM) brain tumours acquire resistance to treatment, leading 100% of primary tumours to recur. The two working hypotheses of our group are that either individual subclones from the primary tumour are inherently resistant and selected for during treatment, or that transcriptional reprogramming enables cells to adapt their phenotype and become resistant.
To understand more about the mechanism of resistance in GBM, I am using a novel technique known as nanobiopsy that allows us to extract cytoplasmic material from single brain tumour cells without killing them. Using this technique we can now, for the first time, longitudinally track and biopsy single cells sequentially during treatment, thereby characterising how the transcriptional profile of individual cells change. To achieve this, I am sequencing sub-single cell RNAseq libraries, created from cytoplasm nanobiopsied pre and post treatment, using the SMART-seq2 and NEXTeraXT workflow.
The biggest challenge that had to be overcome was the amplification of such small amounts of RNA (<1pg) into adequate cDNA for use in NGS library preparation. Dr Iain Macaulay, at the Earlham Institute, assisted with this part of the project. By acquiring a travel grant by the Harold Hyam Wingate Foundation, I was able to visit his state-of-the-art laboratory and worked closely with experts in his single cell technology group to optimise the SMART-seq2 protocol for ultra-low RNA amounts. We have successfully obtained sufficient amounts of cDNA for downstream library preparation, from a starting material of as low as 0.5pg of RNA (approx. 5-10% of a cell’s RNA).
Apart from achieving our very challenging aim, my visit to the Earlham Institute was very inspiring. I spent time preparing RNAseq libraries using different robots, I learnt a quick and easy way to check the sorting alignment on FACS Melody prior to sorting, and I have brainstormed and discussed other alternative ways of amplifying the nanobiopsies in order to get information beyond the coding RNA species.
Earlham Institute: https://www.earlham.ac.uk/
Twitter page: @EarlhamInst
Keeping our commitment to update and strengthen our skills on Omics data analyses, our Bioinformatics Research Officer, Dr Elton Vasconcelos, has recently attended a Proteomics Bioinformatics Course provided by EMBL-EBI jointly with the Wellcome Genome Campus Advanced Courses at Hinxton, UK. The course included a mix of both theoretical lectures and practical sessions aimed at hands-on training in the basics of mass spectrometry and proteomics bioinformatics, search engines and post-processing software, quantitative approaches, MS data repositories, the use of public databases for protein analysis, annotation of subsequent protein lists and incorporation of information from molecular interaction and pathway databases.
Dr Vasconcelos has identified proteomics as one of the key omics approaches that he wants to develop further expertise in. He hugely benefitted from attending the EBML-EBI course, improving his understanding of the data, as well as how to better perform analyses using cutting-edge tools. He has already started collaborating on proteomics data analysis efforts for different projects in both Dr Julie Aspden and Dr Niamh Forde research groups. His background in molecular biology/biochemistry and bioinformatics definitely helps him making the most of this new skill acquisition, enabling him to enhance a niche skill set within LeedsOmics.
The LeedsOmics Research Symposium 2019 on May 13th, 2019 was a great success again this year, full of great talks by talented researchers with an emphasis on genomics, transcriptomics, translatomics and proteomics at the University of Leeds. We hosted two keynote speakers: Dr Michael Barnes (Queen Mary University of London) and Prof Claire Eyers (University of Liverpool), who delighted us with fantastic overviews on machine learning applied to omics-derived clinical data and paradigm shifts in our understanding of protein phosphorylation, respectively. Attendees (PhD students, postdocs, technicians, and academics) had plenty of opportunities to chat about omics-related science during coffee/lunch breaks, a stimulating poster session, and wine and cheese reception.
Congratulations to Alysha Taylor on winning the best oral presentation award and to Ioannis Tsagakis on winning the best poster presentation award at LeedsOmics Research Symposium 2019.