 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 09, 2013 |
| Title |
Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene |
| Organism |
Symphysodon aequifasciata |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the effects of the combination of two PAHs, benzo[a]pyrene (0.5μg/L) and phenanthrene (50μg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48h of exposure. The cDNA libraries were constructed according to the SOLiDTM SAGETM protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program (AmiGO v.1.8). The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and a greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated genes (46%), in the experimental group compared to the control group. Out of this total, 327 genes were successfully categorized, 174 down-regulated and 153 up-regulated genes, using gene ontology tool. The final confidence gene network, analyzed in STRING, was composed by 199 nodes of proteins, 124 of them resulted in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, changes in oxidation-reduction processes, disturbances of intracellular signaling and changes in the immune response of discus fish. Also the gene network interactions have showed no central interplay cluster, exhibiting interconnected clusters interactions and sparsely connected sub-networks. These findings highlight that even an acute and sublethal exposure of PAHs can cause metabolism changes that may affect this fish species survival rates. Our findings using the SAGE-method and the SOLiD sequencer showed that this is a powerful tool for gene expression analysis in discus fish, a non-model organism.
|
| |
|
| Overall design |
Transcriptome analysis of differentially expressed genes in liver in benzo[a]pyrene and phenanthrene-exposed and non-exposed fish (N=6 per treatment)
|
| |
|
| Contributor(s) |
Lemgruber RS, Marshall NA, Ghelfi A, Fagundes DB, Val AL |
| Citation(s) |
24312524 |
| |
| Submission date |
Sep 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Renato de Souza Pinto Lemgruber |
| E-mail(s) |
renatospl@hotmail.com
|
| Organization name |
University of Queensland
|
| Lab |
AIBN
|
| Street address |
Building 75,Cnr College Rd & Cooper Rd
|
| City |
Brisbane |
| State/province |
QLD |
| ZIP/Postal code |
4072 |
| Country |
Australia |
| |
|
| Platforms (1) |
| GPL17765 |
AB SOLiD 3 Plus System (Symphysodon aequifasciata) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA221346 |
| SRA |
SRP030414 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE51149_RAW.tar |
40.0 Kb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
