Bioinformatics Technologies for Next Generation Sequencing Data in Animal Science Research

Le Yu, Jacqueline Smith, Almas Gheyas, Dave Burt

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Nowadays the Next Generation Sequencing (NGS) as a novel high-throughput sequencing technology has developed significantly. The vast amount of data generated by these technologies requires proper methods for the extraction of robust quantitative measures and processes. This poster includes the bioinformatics technologies and statistical methods applied to NGS data in animal science research. It also introduces some examples of results from our NGS based research projects since 2009.
Three projects are presented in this poster.
1) Activation of novel molecular circuits involved in epigenetic re-modelling in the Ovine Pars Tuberalis in response to long photoperiods revealed by RNASeq
2) A comparison of immune responses to avian influenza infection in ducks and chickens: a focus on the interferon-induced transmembrane proteins
3) Development of a high density 600K SNP genotyping array for chicken

The analysis is based on RNASeq data, miRNASeq data, SNP data, MeDIPSeq data and BisulfiteSeq data for chicken, sheep, duck and quail. Methods include gene annotation, sequence alignment, transcriptome assembly, alternative splicing detection, transcript factor analysis, microRNA target prediction, genetic variation detection, differential expressed gene identification, epigenetic changes classification, gene clustering and genome visualisation etc.

The results show that NGS data has been widely used in the animal science research. Using bioinformatics and statistical analysis based on these data we identified a large number of dynamic changes of DNA and mRNA involved in molecular controls, immune response, genetic variation and epigenetic remodelling. Many of them have been validated in the lab experiments.
Original languageEnglish
Title of host publicationSULSA's 2013 Research Symposium
Publication statusPublished - 2013
EventSULSA [Scottish Universities Life Sciences Alliance] Research Sumposium - The New Genomics: Knowledge, Health & Society: - JMCC, University of Edinburgh, Edinburgh, United Kingdom
Duration: 9 Sep 20139 Sep 2013

Conference

ConferenceSULSA [Scottish Universities Life Sciences Alliance] Research Sumposium - The New Genomics: Knowledge, Health & Society:
CountryUnited Kingdom
CityEdinburgh
Period9/09/139/09/13

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