Open Access Highly Accessed Research article

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro

Nicolas C Nalpas1, Stephen DE Park1, David A Magee1, Maria Taraktsoglou1, John A Browne1, Kevin M Conlon2, Kévin Rue-Albrecht1, Kate E Killick1, Karsten Hokamp3, Amanda J Lohan4, Brendan J Loftus4, Eamonn Gormley5, Stephen V Gordon24 and David E MacHugh14*

Author Affiliations

1 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Dublin 4, Ireland

2 UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Dublin 4, Ireland

3 Smurfit Institute of Genetics, Trinity College Dublin, Trinity College, Dublin, Ireland

4 UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Dublin 4, Ireland

5 Tuberculosis Diagnostics and Immunology Research Centre, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Dublin 4, Ireland

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BMC Genomics 2013, 14:230  doi:10.1186/1471-2164-14-230

Published: 8 April 2013

Additional files

Additional file 1: Table S1:

RNA-seq libraries information. The indexed adapter sequence, animal sample ID, sample treatment, pooling strategy, and sequencing read information (number and percentage) before and after data filtering are given for each RNA-seq library.

Format: XLSX Size: 14KB Download file

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Additional file 2: Figure S1:

Density plot of the distribution of reads per gene. Density plots of the number of sequence reads (in log10 space) per gene for each RNA-seq library sample.

Format: PNG Size: 19KB Download file

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Additional file 3: Table S2:

The list of all significant differentially expressed genes detected following M. bovis infection based on RNA-seq sense strand data. For each differentially expressed gene is shown its gene name, log2 fold-change, P-value, adjusted P-value (Benjamini-Hochberg correction), description and Ensembl gene ID. The biomaRt package and the B. taurus reference genome were used to obtain gene names and gene descriptions. Genes without names or descriptions are stated here as “not available”.

Format: XLSX Size: 322KB Download file

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Additional file 4: Table S3:

GO categories identified using IPA based on RNA-seq sense strand data. The top ranking GO categories identified by IPA based on RNA-seq sense strand data are ranked according to P-values.

Format: XLSX Size: 49KB Download file

Open Data

Additional file 5: Table S4:

Significant canonical pathways identified using IPA based on RNA-seq sense strand data. The canonical pathways identified by IPA based on RNA-seq sense strand data are ranked according to P-values. The ratio indicates the number of differentially expressed genes involved in each canonical pathway divided by the total number of genes/molecules within each pathway according to the IPA Knowledge Base.

Format: XLSX Size: 56KB Download file

Open Data

Additional file 6: Table S5:

The list of all significant differentially expressed genes detected following M. bovis infection based on RNA-seq antisense strand data. For each differentially expressed gene is shown its gene name, log2 fold-change, P-value, adjusted P-value (Benjamini-Hochberg correction), description and Ensembl gene ID. The biomaRt package and the B. taurus reference genome were used to obtain gene names and gene descriptions. Genes without names or descriptions are stated here as “not available”.

Format: XLSX Size: 102KB Download file

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Additional file 7: Figure S2:

Integrative Genomics Viewer (IGV) screen capture of reads mapping to SPTB gene. This figure shows the distribution of sense (represented in red) and antisense (represented in blue) strand reads that mapped to the 3′ end of spectrin, beta, erythrocytic gene (SPTB).

Format: PNG Size: 125KB Download file

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Additional file 8: Table S6:

GO categories identified using IPA based on RNA-seq antisense strand data. The top ranking GO categories identified by IPA based on RNA-seq antisense strand data are ranked according to P-values.

Format: XLSX Size: 23KB Download file

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Additional file 9: Table S7:

Significant canonical pathways identified using IPA based on RNA-seq antisense strand data. The canonical pathways identified by IPA based on RNA-seq antisense strand data are ranked according to P-values. The ratio indicates the number of differentially expressed genes involved in each canonical pathway divided by the total number of genes/molecules within each pathway according to the IPA® Knowledge Base.

Format: XLSX Size: 45KB Download file

Open Data

Additional file 10: Figure S3:

Multi-dimensional scale plot of all M. bovis-infected and control samples based on Microarray data. Dimension 1 and dimension 2 separate all 12 samples based on the expression value of the 11,790 probes (based on microarray data only) that passed all data filtering criteria prior to differential gene expression analysis.

Format: PNG Size: 14KB Download file

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Additional file 11: Table S8:

The list of all significant differentially expressed genes detected following M. bovis infection based on microarray data. For each differentially expressed gene is shown its gene name, log2 fold-change, P-value, adjusted P-value (Benjamini-Hochberg correction), description and Ensembl gene ID. The biomaRt package and the B. taurus reference genome were used to obtain gene names and gene descriptions. Genes without names or descriptions are stated here as “not available”.

Format: XLSX Size: 249KB Download file

Open Data

Additional file 12: Table S9:

List of all significant differentially expressed genes detected following M. bovis infection common to both microarray and RNA-seq sense strand data. For each differentially expressed gene is shown its Ensembl gene ID, gene name, description, log2 fold-change, P-value and adjusted P-value (Benjamini-Hochberg correction) based on microarray and RNA-seq sense strand data. The biomaRt package and the B. taurus reference genome were used to obtain gene names and gene descriptions. Genes without names or descriptions are stated here as “not available”.

Format: XLSX Size: 183KB Download file

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Additional file 13: Figure S4:

Density plots of log2 mean CPM and log2 mean hybridisation intensities for differentially expressed genes unique and common to both platforms. This analysis was performed for each platform/treatment group. DEG, differentially expressed genes.

Format: PNG Size: 17KB Download file

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Additional file 14: Table S10:

GO categories identified using IPA based on microarray data. The top ranking GO categories identified by IPA based on microarray data are ranked according to P-values.

Format: XLSX Size: 35KB Download file

Open Data

Additional file 15: Table S11:

GO categories identified using IPA based on differentially expressed genes common to both microarray and RNA-seq sense strand data. The top ranking GO categories identified by IPA based on differentially expressed genes common to both microarray and RNA-seq sense strand data are ranked according to P-values.

Format: XLSX Size: 26KB Download file

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Additional file 16: Table S12:

Significant canonical pathways identified using IPA based on microarray data. The canonical pathways identified by IPA based on microarray data are ranked according to P-values. The ratio indicates the number of differentially expressed genes involved in each canonical pathway divided by the total number of genes/molecules within each pathway according to the IPA® Knowledge Base.

Format: XLSX Size: 57KB Download file

Open Data

Additional file 17: Table S13:

Significant canonical pathways identified using IPA based on differentially expressed genes common to both microarray and RNA-seq sense strand data. The canonical pathways identified by IPA based on differentially expressed genes common to both microarray and RNA-seq sense strand data are ranked according to P-values. The ratio indicates the number of differentially expressed genes involved in each canonical pathway divided by the total number of genes/molecules within each pathway according to the IPA® Knowledge Base.

Format: XLSX Size: 31KB Download file

Open Data