Open Access Research article

Global endometrial transcriptomic profiling: transient immune activation precedes tissue proliferation and repair in healthy beef cows

Cathriona Foley12, Aspinas Chapwanya23, Christopher J Creevey1, Fernando Narciandi2, Derek Morris4, Elaine M Kenny4, Paul Cormican4, John J Callanan5, Cliona O’Farrelly2 and Kieran G Meade1*

Author Affiliations

1 Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Co, Meath, Ireland

2 Comparative Immunology Group, School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland

3 Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria, South Africa

4 TrinSeq, Trinity Genome Sequencing Laboratory, Institute of Molecular Medicine (IMM), Trinity College Dublin, Dublin 2, Ireland

5 UCD School of Veterinary Medicine, Dublin 4, Ireland

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BMC Genomics 2012, 13:489  doi:10.1186/1471-2164-13-489

Published: 18 September 2012

Additional files

Additional file 1:

a: Alignment of reads to the bovine genome with TopHat. TopHat calls the Bowtie software to align reads to the bovine genome. This table shows the combined Bowtie output from paired end reads for all samples that are reported in the “logs” output from TopHat. b: Summarization of read counts for each gene with HtSeq-Count. The numbers of reads representing genes annotated in Ensembl and subsequently filtered for downstream analysis. c: Normalised library sizes with TMM-EdgeR. The number of reads used for each animal is shown before and after normalisation using TMM-EdgeR.

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Additional file 2:

Primer details for candidate and reference genes used in real-time RT-qPCR. ACTB and GAPDH were the reference genes used to calculate relative fold changes for all other candidate genes.

Format: DOC Size: 43KB Download file

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