Gene Expression

The Gene Expression Unit provides DNA microarray services, ranging from experimental design over complete sample processing to expert advice on data analysis. We are an Affymetrix Core Lab with reference status for GeneChip technology in Portugal since 2002.

Services include:

Gene Expression Profiling (3’ IVT, Gene, Exon and Tiling arrays)
Genotyping, CNV (500K array set and SNP 6.0 array)
Cytogenetics (Whole-genome 2.7M array)
MicroRNA Profiling (miRNA array)
ChIP-on-Chip (Tiling arrays)
Custom array projects
RNA and DNA quality analyses (Bioanalzyer)

Equipment:

Scanner 3000 7G with Autoloader (*)
Fluidics Station 450 (*)
Hybridization Oven 640
Bioanalyzer 2100
Affymetrix and Partek Genomics Suite software

(*) Financed by Fundação para a Ciência e Tecnologia (Programa Nacional de Re-Equipamento Científico).

Publications including data produced by the unit:

1. Becker JD, Boavida LC, Carneiro J, Haury M, Feijó JA: Transcriptional profiling of Arabidopsis tissues reveals the unique characteristics of the pollen transcriptome. Plant Physiology 2003, 133(2): 713–725 Link pdf
2. Pina C, Pinto F, Feijó JA, Becker JD: Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation. Plant Physiology 2005, 138(2): 744–756 Link pdf
3. Sessa G, Carabelli M, Sassi M, Ciolfi A, Possenti M, Mittempergher F, Becker J, Morelli G, Ruberti I: A dynamic balance between gene activation and repression regulates the shade avoidance response in Arabidopsis. Genes and Development 2005, 19(23): 2811–2815 Link pdf
4. Teixeira MC, Fernandes AR, Mira NP, Becker JD, Sá-Correia I: Early transcriptional response of Saccharomyces cerevisiae to stress imposed by the herbicide 2,4-dichlorophenoxyacetic acid. FEMS Yeast Research 2006, 6(2): 230–248 Link pdf
5. Marsch-Martinez N, Greco R, Becker JD, Dixit S, Bergervoet JH, Karaba A, de Folter S, Pereira A: BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways. Plant Molecular Biology 2006, 62(6): 825–843 Link pdf
6. Schiedlmeier B, Santos AC, Ribeiro A, Moncaut N, Lesinski D, Auer H, Kornacker K, Ostertag W, Baum C, Mallo M, Klump H: HOXB4's road map to stem cell expansion. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(43): 16952–16957 Link pdf
7. Carabelli M, Possenti M, Sessa G, Ciolfi A, Sassi M, Morelli G, Ruberti I: Canopy shade causes a rapid and transient arrest in leaf development through auxin-induced cytokinin oxidase activity. Genes and Development 2007, 21(15): 1863-1868 Link pdf
8. Igreja C, Courinha M, Cachaço AS, Pereira T, Cabeçadas J, da Silva MG, Dias S: Characterization and clinical relevance of circulating and biopsy-derived endothelial progenitor cells in lymphoma patients. Haematologica 2007, 92(4): 469-77 Link pdf
9. Carapau D, Kruhofer M, Chatalbash A, Orengo JM, Mota MM, Rodriguez A: Transcriptome profile of dendritic cells during malaria: cAMP regulation of IL-6. Cellular Microbiology 2007, 9(7): 1738–1752. Link web
10. Rodrigues RF, Roque L, Krug T, Leite V: Poorly differentiated and anaplastic thyroid carcinomas: chromosomal and oligo-array profile of five new cell lines. British Journal of Cancer 2007, 96: 1237-1245. Link pdf
11. Igreja C, Fragoso R, Caiado F, Clode N, Henriques A, Camargo L, Reis EM, Dias S: Detailed molecular characterization of cord blood-derived endothelial progenitors. Experimental Hematology 2008, 36(2): 193-203. Link web
12. Batista R, Saibo N, Lourenço T, Oliveira MM: Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proceedings of the National Academy of Sciences of the United States of America 2008, 105(9): 3640-3645. Link pdf
13. Trindade A, Kumar SR, Scehnet JS, Lopes-da-Costa L, Becker J, Jiang W, Liu R, Gill PS, Duarte A: Overexpression of Delta-Like 4 induces arterialization and attenuates vessel formation in developing mouse embryos. Blood 2008, 112: 1720-1729. Link pdf
14. Borges F, Gomes G, Gardner R, Moreno N, McCormick S, Feijó JA, Becker JD: Comparative transcriptomics of Arabidopsis thaliana sperm cells. Plant Physiology 2008, 148:1168-1181. Link web
15. Pina C, May G, Gardner R, Soneji S, Hong D, Enver T: MLLT3 regulates early human erythroid and megakaryocytic cell fate. Cell Stem Cell 2008, 2: 264-273. Link web
16. Mira NP, Lourenço AB, Fernandes AR, Becker JD, Sá-Correia I: The RIM101 pathway has a role in Saccharomyces cerevisiae adaptive response and resistance to propionic acid and other weak acids. FEMS Yeast Research 2009, 9: 202-216. Link web
17. Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM: Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli. Microbiology 2009, 155: 813–824. Link web
18. Albuquerque SS, Carret C, Grosso AR, Tarun AS , Peng X, Kappe SHI, Prudêncio M, Mota MM: Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics 2009, 10: 270. Link pdf