Type

Journal Article

Authors

David E. MacHugh
Stephen V Gordon
Eamonn Gormley
Cliona O'Farrelly
Kieran G Meade
Karsten Hokamp
Stephen D. E. Park
Kate E Killick
David A. Magee
John A Browne
and 3 others

Subjects

Veterinary

Topics
tuberculosis transcriptional profiling microarray mycobacterium bovis cattle high throughput peripheral blood leukocytes holstein friesian rna seq biomarker peripheral blood systems analysis gene expression profiles

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis. (2014)

Abstract Bovine tuberculosis, caused by infection with Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including gene expression microarrays and RNA-sequencing (RNA-seq), has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analyzed the peripheral blood leukocyte (PBL) transcriptome of eight natural M. bovis-infected and eight age- and sex-matched non-infected control Holstein-Friesian animals using RNA-seq. In addition, we compared gene expression profiles generated using RNA-seq with those previously generated using the high-density Affymetrix(®) GeneChip(®) Bovine Genome Array platform from the same PBL-extracted RNA. A total of 3,250 differentially expressed (DE) annotated genes were detected in the M. bovis-infected samples relative to the controls (adjusted P-value ≤0.05), with the number of genes displaying decreased relative expression (1,671) exceeding those with increased relative expression (1,579). Ingenuity(®) Systems Pathway Analysis (IPA) of all DE genes revealed enrichment for genes with immune function. Notably, transcriptional suppression was observed among several of the top-ranking canonical pathways including Leukocyte Extravasation Signaling. Comparative platform analysis demonstrated that RNA-seq detected a larger number of annotated DE genes (3,250) relative to the microarray (1,398), of which 917 genes were common to both technologies and displayed the same direction of expression. Finally, we show that RNA-seq had an increased dynamic range compared to the microarray for estimating differential gene expression.
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Full list of authors on original publication

David E. MacHugh, Stephen V Gordon, Eamonn Gormley, Cliona O'Farrelly, Kieran G Meade, Karsten Hokamp, Stephen D. E. Park, Kate E Killick, David A. Magee, John A Browne and 3 others

Experts in our system

1
David E. MacHugh
University College Dublin
Total Publications: 82
 
2
Stephen V. Gordon
University College Dublin
Total Publications: 40
 
3
E Gormley
University College Dublin
Total Publications: 68
 
4
Cliona O'Farrelly
Trinity College Dublin
Total Publications: 147
 
5
Kieran G Meade
Teagasc
Total Publications: 58
 
6
Karsten Hokamp
Trinity College Dublin
Total Publications: 47
 
7
Stephen D. E. Park
University College Dublin
Total Publications: 35
 
8
Kate E Killick
University College Dublin
Total Publications: 14
 
9
David A. Magee
University College Dublin
Total Publications: 47
 
10
John A Browne
University College Dublin
Total Publications: 73