**Enchytraeus albidus** microarray : enrichment, design, annotation and database (EnchyBASE)
| Autor: | Mónica J.B. Amorim, Wim De Coen, Dick Roelofs, Sara C. Novais, Joel P. Arrais, Amadeu M.V.M. Soares, Pedro Lopes, Tine Vandenbrouck |
|---|---|
| Přispěvatelé: | Animal Ecology, Amsterdam Global Change Institute |
| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Microarrays
lcsh:Medicine 010501 environmental sciences Toxicology computer.software_genre 01 natural sciences Transcriptomes Databases Genetic Cluster Analysis lcsh:Science Oligonucleotide Array Sequence Analysis Expressed Sequence Tags Genetics 0303 health sciences Expressed sequence tag Multidisciplinary Ecology Contig Database Gene Ontologies Genomics Soil Ecology Terrestrial Environments Functional Genomics GenBank Functional genomics Research Article DNA Complementary Genetic Toxicology Molecular Sequence Data Biology 03 medical and health sciences Genome Analysis Tools Metals Heavy Animals Oligochaeta Pesticides Terrestrial Ecology KEGG 030304 developmental biology 0105 earth and related environmental sciences Internet Sequence Assembly Tools Base Sequence cDNA library Microarray analysis techniques lcsh:R Computational Biology Sequence Analysis DNA Microarray Analysis Suppression subtractive hybridization lcsh:Q Human medicine Genome Expression Analysis computer Environmental Protection Ecological Environments |
| Zdroj: | PLoS ONE Novais, S C, Arrais, J, Lopes, P, Vandenbrouck, T, de Coen, W, Roelofs, D, Soares, A M V M & Amorim, M J B 2012, ' Enchytraeus albidus microarray: Enrichment, design, annotation and database (EnchyBASE). ', PLoS ONE, vol. 7 (4), pp. e34266 . https://doi.org/10.1371/journal.pone.0034266 PLoS ONE, Vol 7, Iss 4, p e34266 (2012) PLoS ONE, 7 (4). Public Library of Science Repositório Científico de Acesso Aberto de Portugal Repositório Científico de Acesso Aberto de Portugal (RCAAP) instacron:RCAAP |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0034266 |
| Popis: | Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value ≤ 10(-5)) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies. published |
| Databáze: | OpenAIRE |
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