iEOS2015 – Pre-meeting NBAF Workshop http://environmentalomics.org/ieos2015-workshops/ #iEOS2015



NERC Biomolecular Analysis Facility (NBAF) technology workshops


Additional details of workshop

A half-day training workshop will be held on 6th July, from 12:30-16:00, and delivered by staff from the NERC Biomolecular Analysis Facility (NBAF). NBAF delivers genomic and metabolomics data and analysis to NERC researchers via Services and Facilities that are specifically geared towards the research within the natural environment. By the end of the workshop, each student will have an understanding of the fundamentals of the analysis methods used in relation to a specific topic and will have undertaken a practical analysis of trial data.

Each student will pick one of four parallel topics:

Gene expression analysis: Students will learn the principles behind the design of a gene expression experiment using RNA sequencing technologies, including statistical design and quality control of samples. The students will analyse case examples within a computing practical exercise and learn familiarity with basic analysis tools in Linux and R to map sequence reads against a genome and to identify differentially expressed genes.

Metabolomics workshop: NBAF-B staff will provide a broad introduction to metabolomics, from experimental design over common analytical techniques to statistical approaches. This year a special emphasis will be placed on experimental design (e.g. biological classes, sample numbers, biological versus technical replication, quality assessment) and sample preparation (especially realistic methods for rapidly quenching the metabolism) for different types of samples – an especially important field considering the diversity of organisms in environmental metabolomics. Participants are invited to suggest specific sample types in advance.

Restriction-site Associated DNA (RAD) Data Analysis: NBAF staff will run this workshop, including an introduction to RAD sequencing in the environmental genomics context and hands-on analyses of a representative RAD dataset using popular software (e.g. STACKS). No prior knowledge of high throughput sequencing data analysis is required but experience with the Linux environment and basic command line tools would be advantageous.

eDNA & metabarcoding: NBAF-S staff will describe applications of environmental DNA (eDNA) analysis including diet analysis and biodiversity surveys. The session will introduce methods to generate and analyse metabarcoding data (DNA barcodes from samples containing many species, generated using NGS) from environmental DNA samples (trace DNA from water/soil/faeces). We will work on an example data set using popular command-line tools to go from sequence reads to taxonomic data.

Heavy metals are essential for life, however, paradoxically exploitation of land for mineral extraction and manufacturing industry results in the release of large quantities of heavy metals that can be toxic to the natural environment. My research portfolio is designed to exploit state-of-the-art genomic, proteomic and metabolomic techniques to study the mechanisms by which biological systems handle heavy metals assessing: their impact as pollutants, their involvement in disease and the basic mechanisms by which they are bound within biological systems.

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