Measurement and analysis of mRNAs, long non-coding RNAs and microRNAs using next generation sequencing (RNASeq)

Aims:  The rapid reductions in the price of sequencing has meant that RNA sequencing (RNAseq) is replacing microarrays as the option of choice for measuring the transcriptome. This one day course is designed for scientists and clinicians with little or no experience in RNASeq. The course aims to provide the experimental and bioinformatics skills required to prepare samples, quantify the levels of known/novel mRNAs, long intergenic non-coding RNAs and miRNAs using next generation sequencing data.  We assume that sequencing will be performed by an external provider and will provide advice in this area. The course is computer based and will involve a combination of presentations/exercises to analyse 'actual' next generation sequencing data using publically available programmes. This course is designed to complement the ChIPseq course. 

  • Overview on mRNAs, long non-coding RNAs and microRNAs
  • Introduction to RNA databases (Ensembl, RefSeq, GenBank and miRBase)
  • RNA isolation techniques and quality assessment
  • Overview of next generation sequencing platforms 
  • Introduction to data file formats (FASTQ, BAM, GTF and BED files)
  • Analysis of the quality of sequence data (FASTQC)
  • Mapping of RNA data onto a reference genome using HISAT2 and HTseq-count
  • Visualisation and analysis of sequencing data using the IGV genome browsers
  • Quantification of known RNA species using CuffDiff and DEseq
  • Functional annotation using Genesis and DAVID pathway analysis

Dates and location:

Thursday 21st October 2021 - On-line course (Maximum 8 people)

Tuesday 16th December 2021 - On-line course (Maximum 8 people)

Cost: £249 

For reservations contact m.a.lindsay@bath.ac.uk

Course Feedback (Overall 4.4/5.0 from > 450 delegates)

'Excellent, great value - pitch was perfect, useful for beginners and someone with moderate levels of knowledge'

'Good one day course'

'Excellent. Learnt a lot'

'Good general overview. Manual is excellent'

'Very informative but almost too intense for one day'

 Course Trainers

Professor Mark A Lindsay 

Mark Lindsay is Professor of Molecular and Computational Pharmacology at the University of Bath  He obtained a BA in Natural Sciences from Cambridge University and a PhD investigating the mechanism of insulin release from Nottingham in 1991. Following an initial post-doctoral position in renal disease, he moved to the National Heart and Lung Institute, Imperial College London in 1994 where he investigated the mechanisms regulating the inflammatory response in the airways and lung. Between 2001 and 2005 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs and antisense for target discovery and as novel therapeutics.  Since returning to academia in 2005, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon examining the role of the transcriptome in the inflammation associated with multiple diseases. Professor Lindsay has recently undertaken a 12 month secondment as the acting Head of Biology at the MRC Nucleic Acid Therapy Accelerator at the Harwell Science Campus (near Oxford). The nucleic acid therapy accelerator (NATA) is a new UK research initiative with a mission to accelerate the development of nucleic acid therapeutics, building partnerships with industry and academia from around the world.