Open Access Research article

Transcriptome analysis of porcine PBMCs after in vitro stimulation by LPS or PMA/ionomycin using an expression array targeting the pig immune response

Yu Gao123, Laurence Flori123, Jérome Lecardonnel123, Diane Esquerré123, Zhi-Liang Hu4, Angélique Teillaud123, Gaëtan Lemonnier123, Francois Lefèvre5, Isabelle P Oswald6 and Claire Rogel-Gaillard123*

Author Affiliations

1 INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France

2 CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Domaine de Vilvert, 78350 Jouy-en-Josas, France

3 AgroParisTech, Laboratoire de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France

4 Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011-3150, USA

5 INRA, UR892 de Virologie et Immunologie Moléculaires, 78350 Jouy-en-Josas, France

6 INRA, UR66 de Pharmacologie-Toxicologie, 180 chemin de Tournefeuille, BP 93173, 31000 Toulouse, France

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BMC Genomics 2010, 11:292  doi:10.1186/1471-2164-11-292

Published: 11 May 2010

Additional files

Additional file 1:

Detailed information of probes in the Porcine SLA-RI oligonucleotide set. The file SLA_RI_Table_S1.xls is an excel file, which contains the detailed information and GO annotation information for the genes or probes included in the SLA-RI set.

Format: XLS Size: 3.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

List of KEGG pathways represented in the SLA_RI set. The file SLA_RI_Table_S2.doc is a word file, which contains the KEGG pathways represented in the SLA-RI.

Format: DOC Size: 71KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 3:

List of differentially expressed probes in opposite directions according to stimulation. The file SLA_RI_Table_S3.doc is a word file, which contains the gene list of differentially expressed probes in opposite directions according to stimulation from hierarchical clustering (HCL) analysis.

Format: DOC Size: 145KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 4:

Hierarchical clustering of the 316 probes. The file SLA_RI_Figure_S4.png is a portable network graphics file, which shows hierarchical clustering of the 316 probes that were found differentially expressed after LPS and PMA/ionomycin stimulations.

Format: PNG Size: 344KB Download file

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Additional file 5:

LPS-related gene networks. The file SLA_RI_Table_S5.xls is an excel file, which contains the network list obtained for LPS-related gene analysis.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 6:

Details of KEGG biological pathways for genes differentially expressed with LPS or PMA/ionomycin stimulation. The file SLA_RI_Table_S6.doc is a word file, which contains the detailed information of KEGG pathways for genes differentially expressed with LPS or PMA/ionomycin stimulation.

Format: DOC Size: 90KB Download file

This file can be viewed with: Microsoft Word Viewer

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Additional file 7:

PMA/ionomycin-related gene networks. The file SLA_RI_Table_S7.xls is an excel file, which contains the network list obtained for PMA/ionomycin-related gene analysis.

Format: XLS Size: 52KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

Comparison of fold change of gene expression level between microarray and qRT-PCR experiments. The file SLA_RI_Table_S8.doc is a word file, which contains comparison results between microarray and qRT-PCR experiments.

Format: DOC Size: 41KB Download file

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Additional file 9:

Detailed information of differentially expressed genes after LPS or PMA/ionomycin stimulation. The file SLA_RI_Table_S9.xls is an excel file which contains two sheets. The "LPS" sheet contains the detailed information on differentially expressed genes after LPS stimulation, and the "PMA_ionomycin" sheet contains the detailed information on differentially expressed genes after PMA/ionomycin stimulation.

Format: XLS Size: 512KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

Hybridization design. The file SLA_RI_Figure_S10.png is a portable network graphics file, which shows the hybridization design used in this study to investigate the differentially expressed genes after LPS and PMA/ionomycin stimulations. Each arrow represents one microarray with a reversed labeling of cDNAs by Cy3 or Cy5. Arrow heads represent Cy5 and arrows point in the Cy3 to Cy5 direction.

Format: PNG Size: 18KB Download file

Open Data