|
| Status |
Public on Jul 30, 2012 |
| Title |
high treatment day1 replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Coral after 1 day of high treatment exposure replicate 1
|
| Organism |
Acropora millepora |
| Characteristics |
sample type: adult coral in symbiosis with dinoflagellate
acidification treatment: pH 7.6-7.7
time: 1 day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample using Trizol (Invitrogen) following manufacturer’s instructions. The integrity and quality of total RNA was assessed using a Bioanalyzer (Agilent Technology). Only samples showing intact RNA were used for probe construction.
|
| Label |
Cy5
|
| Label protocol |
cDNA probe synthesis was performed from 1000ng total RNA using Superscript Reverse Transcripase (Invitrogen) and the Genisphere 900 3DNA Dendrimer from a Genisphere 3DNA-900 microarray kit according to the manufacturers’ instructions.
|
| |
|
| Channel 2 |
| Source name |
reference sample for coral
|
| Organism |
Acropora millepora |
| Characteristics |
sample type: reference sample of pooled control and time zero adult corals
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample using Trizol (Invitrogen) following manufacturer’s instructions. The integrity and quality of total RNA was assessed using a Bioanalyzer (Agilent Technology). Only samples showing intact RNA were used for probe construction.
|
| Label |
Cy3
|
| Label protocol |
cDNA probe synthesis was performed from 1000ng total RNA using Superscript Reverse Transcripase (Invitrogen) and the Genisphere 900 3DNA Dendrimer from a Genisphere 3DNA-900 microarray kit according to the manufacturers’ instructions.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized using the Genisphere 900 3DNA kit components (vial 7 buffer) plus human Cot DNA (for blocking) at 42 degrees overnight. Wash: 15 min (2X SSC/ 0.1% SDS at 65 degrees), 15 min 2X SSC RT, 15 min 0.2X SSC .
|
| Scan protocol |
Slides were scanned using AXON GenePix4000B, and and image acquisition and quality control was performed using the software GenePix ® Pro 5.
|
| Data processing |
Normexp background corrected signal intensities were used, also print-tip loess normalization was applied within slides, while scale normalization was applied between slides, in order to ensure that distributions were similar between arrays. As the experimental design for this experiment was a reference microarray design the value represents the normalized log (Channel 1/channel 2).
|
| |
|
| Submission date |
Apr 18, 2011 |
| Last update date |
Jul 30, 2012 |
| Contact name |
Paulina Kaniewska |
| E-mail(s) |
p.kaniewska@uq.edu.au
|
| Organization name |
University of Queensland
|
| Department |
School of Biological Sciences
|
| Street address |
Gehrman Building
|
| City |
St Lucia |
| ZIP/Postal code |
7072 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6941 |
| Series (1) |
| GSE28697 |
Acropora millepora adult samples: Control vs medium and high ocean acidification treatment |
|
