Open Access Highly Accessed Research article

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression

Paul Golby1*, Javier Nunez1, Adam Witney2, Jason Hinds2, Michael A Quail3, Stephen Bentley3, Simon Harris3, Noel Smith1, R Glyn Hewinson1 and Stephen V Gordon4

Author Affiliations

1 Animal Health and Veterinary Laboratories Agency, Woodham Lane, New Haw Addlestone, Surrey KT15 3NB, UK

2 Division of Clinical Sciences, Bacterial Microarray Group, Centre for Infection & Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK

3 The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK

4 UCD School of Veterinary Medicine and UCD Conway Institute, University College Dublin, Dublin 4, Ireland

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BMC Genomics 2013, 14:710  doi:10.1186/1471-2164-14-710

Published: 17 October 2013

Additional files

Additional file 1:

SNPs identified across sequenced strains.

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Additional file 2:

Large deletions identified by NGS in sequenced strains.

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Additional file 3:

Fold change differences in gene expression in M. bovis field isolates 1121, 2451 and 1307 compared to 2122. Cells shaded in red indicate upregulation, green indicate down-regulation and empty cells indicate no change in expression.

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Additional file 4:

Differential expression of RNA transcripts as detected by a tiled oligonucleotide microarray. Up and down arrows indicate fold up- and downregulation, respectively, and empty cells indicate no change in expression. *Strand, A indicates antisense, S, sense and I, intergenic.

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Additional file 5:

Details of oligonucleotides used in PCR, RT-PCR and RLM-RACE experiments.

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