 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2012 |
| Title |
Exploring the potential of a Functional Gene Array (FGA) for fluvial biofilms |
| Platform organisms |
Bacillariophyta; Chlorophyta; Chlamydomonas; Tetradesmus obliquus |
| Sample organisms |
Chlamydomonas reinhardtii; Scenedesmus vacuolatus; environmental samples |
| Experiment type |
Expression profiling by array
|
| Summary |
Microarrays offer a comprehensive tool for a system-wide analysis of cell functioning based on the simultaneous detection of the activity of thousands of genes. While transcriptome analyses are usually related with the study of gene expression and regulation within single species in laboratory experiments or environmental samples, in the present study, the possibility of studying gene expression in river biofilm communities was explored. To this aim a Functional Gene array (FGA), based on consensus sequences from genes of key physiological processes, was designed including 83 functional genes chosen to reflect several essential biochemical pathways and specific stress response pathways. Probes of these genes were designed from consensus sequences from up to 6 microalgal species (diatoms and chlorophytes). Furthermore, species specific probes were included resulting in 1556 unique oligonucleotide probes for 83 different genes. RNA extracted from Chlamydomonas reinhardtii, Scenedesmus vacuolatus and multi-species biofilms was then hybridized to oligonucleotide arrays at different hybridization temperatures (55, 60 and 65ºC). Signal intensity was affected by sequence divergence but results showed that hybridisation temperature of 55ºC allowed a good compromise between cross-hybridization and specificity. Due to the limited number of probes and available sequence information the designed FGAs is at present particularly useful for the comparison of similar biofilms exposed to different conditions in laboratory experimental studies.
|
| |
|
| Overall design |
Nine samples were used, three were extracted from biofilm communities and hybridized at 55, 60 and 65 ºC, respectively; three were extracted from Scenedesmus vacuolatus and hybridized at 55, 60 and 65 ºC, respectively; and the three last ones were extracted from Chlamydomonas reinhardtii and hybridized at 55, 60 and 65 ºC
|
| |
|
| Contributor(s) |
Bonnineau C, Scholz S, Guasch H, Schmitt-Jansen M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jun 22, 2010 |
| Last update date |
Jan 02, 2013 |
| Contact name |
Chloé Bonnineau |
| E-mail(s) |
chloe.bonnineau@udg.edu
|
| Organization name |
Institute of Aquatic Ecology, University of Girona
|
| Street address |
Campus Montilivi, s/n
|
| City |
Girona |
| ZIP/Postal code |
17071 |
| Country |
Spain |
| |
|
| Platforms (1) |
|
| Samples (9)
|
|
| Relations |
| BioProject |
PRJNA128659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22496_RAW.tar |
16.9 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
|
|
|
|
 |
Less...
More...