Open Access Research article

Development of a porcine (Sus scofa) embryo-specific microarray: array annotation and validation

Stephen Tsoi1*, Chi Zhou1, Jason R Grant1, J Alexander Pasternak1, John Dobrinsky2, Philippe Rigault3, Julie Nieminen4, Marc-André Sirard4, Claude Robert4, George R Foxcroft1 and Michael K Dyck1*

Author Affiliations

1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada

2 International Center of Biotechnology, Minitube of America, Mt. Horeb, Wisconsin, USA

3 Gydle Inc, 1363, avenue Maguire Suite 301, Québec, QC, G1T 1Z2, Canada

4 Laboratory of Functional Genomics of Early Embryonic Development, Université Laval, Quebec, QC, G1T 1Z2, Canada

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BMC Genomics 2012, 13:370  doi:10.1186/1471-2164-13-370

Published: 3 August 2012

Additional files

Additional file 1:

EMPV1 initial annotation. Excel file containing the results of the probe sequences annotation with unique gene symbol.

Format: XLS Size: 11.5MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

EMPV1 annotation description. A PDF file containing a detailed explanation of the terms used in additional file 1.

Format: PDF Size: 75KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 3:

Assembly parameter for gene annotation using SeqMan NGen. Text file containing the details of the parameter set up.

Format: TXT Size: 1KB Download file

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Additional file 4:

Probe sequences without GS selected from EMPV1. PDF file containing the probe ID and sequences for re-annotation.

Format: PDF Size: 5.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 5:

Re-annotation of the probe sequences without GS. Excel file containing the results of porcine gene annotation with probe ID, accession number, gene description, gene symbol (sheet 1) and LOC (sheet 2).

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

BLAST search result from NCBI using porcine sequences. Excel file containing porcine sequences with no GS to blast search with human RefSeq RNA database from NCBI. (XLS 36 kb)

Format: XLS Size: 2.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

All GS list from EMPV1. Excel file containing a list of unique GS from EMPV1 after re-annotation of all the unknown probe sequences. Yellow indicates olfactory receptor genes.

Format: XLS Size: 747KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

EMPV1 PANTHER GO analysis. Excel file containing genes with PANTHER Family/Subfamily, GO Molecular Function, GO Biological Process, GO Cellular Component and PANTHER Protein Class that are present on EMPV1 microarray.

Format: XLS Size: 3.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 9:

GS list from Affymetrix and EMPV1 microarray. Excel file containing column of gene symbols only found in Affymetrix and EMPV1 microarray after removing all the common GS.

Format: XLS Size: 563KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

PANTHER GO biological process difference in Affymetrix and EMPV1 porcine microarray. Excel file containing statistical significance of the gene count differences between unique GS from EMPV1 array and Affymetrix porcine array over different categories of biological processes using PANTHER expression tool. Yellow indicates genes over-representated in EMPV1 (p-value <0.05) and Green indicates genes over-representated in Affymetrix (p-value <0.05).

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 11:

Array-array intensity correlation associated with labelled spike-in RNA mixed with labelled COC aRNA. PDF file containing the correlation index from two biological COC samples. A: COC1 labelled with Cy3 and COC1 labelled with Cy5; B: COC2 labelled with Cy3 and COC2 labelled with Cy5; C: COC1 labelled with Cy3 and COC2 labelled with Cy5; D: COC2 labelled with Cy3 and COC1 labelled with Cy5.

Format: PDF Size: 125KB Download file

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Additional file 12:

Positive spot selection in COC microarray. Excel file containing all positive signals higher than the background intensity signal > 6.69 calculated according to Methods.

Format: XLS Size: 3MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 13:

Positive spots selection in embryos microarray. Excel file containing all positive signals higher than the background intensity signal > 6.96 calculated according to Methods.

Format: XLS Size: 3MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 14:

Unique GS list from COC and embryos array data. Excel file containing unique GS from microarray data with genes only found in COC, embryos and both.

Format: XLS Size: 675KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 15:

COC pathways. Excel file containing the result of pathway analysis from PANTHER. Yellow indicates the p-value is significant.

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 16:

OR genes expression in COC and embryos. PDF file containing the spot intensity values extracted from microarray data in COC and embryos related to olfactory receptor gene symbols.

Format: PDF Size: 408KB Download file

This file can be viewed with: Adobe Acrobat Reader

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