Open Access Highly Accessed Research article

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

Aran O’Loughlin12, David J Lynn1, Mark McGee3, Sean Doyle2, Matthew McCabe1 and Bernadette Earley1*

Author Affiliations

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

2 Department of Biology and National Institute for Cellular Biotechnology, National University of Ireland Maynooth, Co. Kildare, Ireland

3 Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland

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BMC Genomics 2012, 13:250  doi:10.1186/1471-2164-13-250

Published: 18 June 2012

Additional files

Additional file 1 :

Table S1.This summary file contains the raw read counts broken down by gene and sample.

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Additional file 2 :

Table S2.Differentially Expressed Genes. This file contains a list of the significantly differentially expressed (FDR < 0.05) genes at each comparison and their human orthologs, when available.

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Additional file 3 :

Table S3.Lane Assignment and Preliminary Analysis of RNA-seq Reads. This file contains a table containing the lane assignments for each sample along with a summary of reads by lane.

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Additional file 4 :

Table S4.Significantly differentially expressed pathways between weaned and control calves.

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Additional file 5 :

Table S5.Over-represented InnateDB pathways involved in the bovine stress response. This file contains a list of pathways identified with InnateDB as being over-represented among the differentially expressed genes for each comparison.

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Additional file 6 :

Table S6.Significantly differentially expressed pathways in weaned calves.

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Additional file 7 :

Table S7.Significantly differentially expressed pathways in control calves.

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Additional file 8 :

Table S8.Alternatively spliced genes. This file contains a list of genes that underwent alternative splicing for each comparison.

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Additional file 9 :

Table S9.Pathways affected by alternative splicing. This file contains a list of pathways identified as over-represented following analysis with alternatively spliced genes.

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Additional file 10 :

Table S10.Significantly over-represented transcription factors based on transcription factor binding sites of up- and down-regulated genes between weaned and control calves. This file contains a table of transcription factors identified as having a role in the regulation of genes differentially expressed between weaned and control animals using oPOSSUM.

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Additional file 11 :

Table S11.Significantly over-represented transcription factors based on transcription factor binding sites of up- and down-regulated genes following weaning. This file contains a table of transcription factors identified as having a role in the regulation of genes differentially expressed following weaning using oPOSSUM.

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Additional file 12 :

Table S12.Significantly over-represented transcription factors based on transcription factor binding sites of up- and down-regulated genes following housing. This file contains a table of transcription factors identified as having a role in the regulation of genes differentially expressed following housing stress using oPOSSUM.

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