|
| Status |
Public on Jan 03, 2008 |
| Title |
whole crab postmoult (Cy3) compared with intermoult (Cy5) rep 3 left |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole crab postmoult
|
| Organism |
Portunus pelagicus |
| Characteristics |
3 individual whole crabs (pooled equally) sampled at the postmoult stage of the moult cycle
|
| Biomaterial provider |
Bribie Island Aquaculture Research Centre
|
| Growth protocol |
Crabs were individually housed in a flowthrough system at an ambient water temperature of 24oC and fed a commercial diet, twice daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole crabs were snap frozen and ground under liquid nitrogen. Total RNA was isolated from each sample using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
10 ug of total RNA (pooled from 3 individuals) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
whole crab intermoult
|
| Organism |
Portunus pelagicus |
| Characteristics |
3 individual whole crabs (pooled equally) sampled at the intermoult stage of the moult cycle
|
| Biomaterial provider |
Bribie Island Aquaculture Research Centre
|
| Growth protocol |
Crabs were individually housed in a flowthrough system at an ambient water temperature of 24oC and fed a commercial diet, twice daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole crabs were snap frozen and ground under liquid nitrogen. Total RNA was isolated from each sample using Trizol reagent as recommended by the manufacturer (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA was DNase treated using RQ1 RNase free DNase (Promega, Madison, WI, USA) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA, USA) as recommended by the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
10 ug of total RNA (pooled from 3 individuals) was converted to cDNA then labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
cDNA was labelled and hybridised to the array using the 3DNA Array 900 MPX expression array detection kit (Genisphere Inc., Hatfield, PA, USA) according to the manufacturer's protocol.
|
| Scan protocol |
Microarray slides were scanned using a white-light ArrayWorx Biochip Reader (Applied Precision, LLC, Issaquah, Washington, USA). ImaGene (BioDiscovery Inc., El Segundo, CA, USA) was then used to process images and create spot intensity reports, while CloneTracker (Biodiscovery Inc.) was used to generate gene ID mapping files and assign gene identification. Final intensity reports were retrieved as raw spot intensities in tab-delimited files.
|
| Description |
Clones were spotted in duplicate on each array (once on the left and once on the right side), providing a technical replicate within each array, analysis of each side of the slide occured individually thus each array has 2 separate data entries one for the left and right. Microarray data analysis was performed by Emphron Informatics (Chapel Hill, Qld, Australia), this information (differential gene expression data) is provided in a separate supplementary file.
|
| Data processing |
The data in the VALUE column was not normalized. The VALUE column contains the log ratios of the raw values for signal intensity for both channels (i.e. Cy3 Signal Mean / Cy5 Signal Mean).
|
| |
|
| Submission date |
Feb 08, 2007 |
| Last update date |
Jan 03, 2008 |
| Contact name |
Anna Viktoria Kuballa |
| E-mail(s) |
[email protected]
|
| Phone |
+61 7 5430 2869
|
| Fax |
+61 7 5430 2881
|
| Organization name |
University of the Sunshine Coast
|
| Department |
Faculty of Science, Health and Education
|
| Street address |
University of the Sunshine Coast
|
| City |
Maroochydore DC |
| State/province |
Queensland |
| ZIP/Postal code |
4558 |
| Country |
Australia |
| |
|
| Platform ID |
GPL4797 |
| Series (1) |
| GSE6997 |
Differential expression analysis of genes relevant to the moult cycle of Portunus pelagicus |
|
