RNASeq 

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. 

Content:
  • 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
  • Visualisation and analysis of sequencing data using the IGV genome browsers
  • Identification and quantification of novel RNA transcripts using StringTie
  • Quantification of known RNA species using CuffDiff/DEseq
  • Functional annotation using Genesis and DAVID pathway analysis

Dates and location:

Wednesday 11th October 2017 - IT Rooms, University of Bath (FULL)

Thursday 7th December 2017 - Just IT Training Rooms nr Aldgate Tube, London 

Thursday 26th April 2018 - Nowgen IT Training Rooms, Manchester

Cost: £349 

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

Courses

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 Pharmacology at the University of Bath and Honorary Senior Scientist at the National Heart and Lung Institute, Imperial College London. 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 2004 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs for the validation of novel drug targets and the identification of new approaches for the delivery of biopharmaceutics. Since returning to academia in 2004, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon the role of miRNAs and long non-coding RNAs in the regulation of the innate immune response and the development of respiratory diseases such as asthma, chronic obstructive pulmonary disease and lung cancer.