|
| Status |
Public on Jan 01, 2015 |
| Title |
Extrapallial fluid from diseased clams - replicate 5 |
| Sample type |
RNA |
| |
|
| Source name |
Extrapallial fluid from diseased clams
|
| Organism |
Ruditapes philippinarum |
| Characteristics |
age: Adult
origin: Aquacultured
clam condition: Diseased
tissue: Hemocytes from extrapallial fluid
|
| Treatment protocol |
Disease diagnostic was performed on shells and clams ranked as either diseased (animals showing signs of brown ring disease) or healthy.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Labeled (Cy3 or Cy5) complementary RNA (cRNA) was synthesized from 150 ng of RNA purified from different tissues of healthy and diseased clams using the Two-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp Labeling) following manufacturer’s protocol
|
| |
|
| Hybridization protocol |
All arrays were hybridized with the same amount of cRNA (300 ng of each Cy3- and Cy5-labeled cRNA).
|
| Scan protocol |
Arrays were scanned with a GenePix 4000B scanner using the suggested Agilent scan settings.
|
| Description |
32
raw data file: 32-44.gpr
|
| Data processing |
Generated fluorescence intensities were normalized to remove within-array and between-array variations using the LIMMA package in R software.
After normalization, probes with intensities less than two-fold background intensities (in all biological replicates) were eliminated from further analysis.
|
| |
|
| Submission date |
Jun 03, 2014 |
| Last update date |
Jan 01, 2015 |
| Contact name |
Bassem Allam |
| Organization name |
Stony Brook University
|
| Lab |
Marine Animal Disease Laboratory
|
| Street address |
School of Marine and Atmospheric Sciences
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794-5000 |
| Country |
USA |
| |
|
| Platform ID |
GPL18750 |
| Series (1) |
| GSE58198 |
Transcriptional changes in Manila clam (Ruditapes philippinarum) in response to brown ring disease |
|
