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| Status |
Public on Aug 15, 2009 |
| Title |
microarray summer mortality insitu oyster |
| Organism |
Magallana gigas |
| Experiment type |
Expression profiling by array
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| Summary |
Summer mortality of the Pacific oyster Crassostrea gigas is the result of a complex interaction between oysters, their environment and pathogens. Heredity appears to be a major factor determining the sensitivity of oysters to summer mortality, allowing resistant (R) and susceptible (S) lines to be produced. We conducted genome-wide expression profiling of R and S gonads during the 3-month period preceding a summer mortality event using a 9K cDNA microarray that we designed. This transcriptional analysis provides new indications to define markers for Quantitative Trait Loci searches and functional studies, and evaluates the potential role of each gene in the resistance to summer mortality
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| Overall design |
For microarray analysis, R and S oysters were sampled four times (dates 1 to 4: May 9, May 25, June 6, and June 20, respectively). On each date, 3 replicates of 8 oysters were sampled from each line (R and S) and the gonads prepared for total RNA extraction. Furthermore, the entire tissues of 10 wild oysters were collected, pooled and homogenized to constitute a single total RNA sample for use as a reference in all slide hybridizations and RT-PCR analysis.
For microarray hybridizations, 5µg of total RNA were directly labeled by reverse transcription and then purified using the Direct ShipShot Labeling kit (Promega). This reaction was performed for each of the 24 gonad samples, with Cy5 (red) incorporation. The reference sample was Cy3-labeled (green) in 24 separate tubes following the same protocol. The 24 Cy3-labeled cDNAs were next pooled, and then divided once more into 24 samples to obtain a homogeneous reference.
Equimolar amounts of cDNA samples and cDNA reference labeled with Cy5 and Cy3, respectively, were SpeedVac evaporated and mixed into a single pool with the hybridization buffer (ChipHyb™ hybridization buffer, Ventana Discovery, Tucson, AZ, USA). They were then co-hybridized on the same microarray slide, in a Ventana hybridization station (Ventana Discovery, Tucson, AZ, USA).
The data submitted here correspond to the mean of the three replicates for each line and each date, representing 8 samples :
gonad_resistant_date1
gonad_sensitive_date1
gonad_resistant_date2
gonad_sensitive_date2
gonad_resistant_date3
gonad_sensitive_date3
gonad_resistant_date4
gonad_sensitive_date4
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| Contributor(s) |
Fleury E, Moal J, Boulo V, Daniel J, Mazurais D, Hénaut A, Corporeau C, Boudry P, Favrel P, Huvet A |
| Citation(s) |
19813056 |
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| Submission date |
Jun 05, 2009 |
| Last update date |
Jul 26, 2013 |
| Contact name |
Arnaud Huvet |
| E-mail(s) |
ahuvet@ifremer.fr
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| Phone |
+33 2 98 22 46 93
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| Fax |
+33 (0)2 98 22 46 53
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| Organization name |
IFREMER
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| Department |
Physiologie Fonctionnelle des Organismes Marins
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| Lab |
Laboratoire de Physiologie des Invertébrés
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| Street address |
Ifremer centre de Brest BP 70
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| City |
Plouzane |
| ZIP/Postal code |
29280 |
| Country |
France |
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| Platforms (1) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA116015 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE16448_RAW.tar |
15.1 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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