|
| Status |
Public on Jan 01, 2013 |
| Title |
13°C/1100 µatm pluteus stage replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Approx. 8,000 pooled larvae from one 13°C/1100 µatm culture replicate
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
Stage: Pluteus
culture conditions: 13°C/1100 µatm
|
| Treatment protocol |
pCO2 within each culture was manipulated by bubbling CO2 gas into seawater as described in Fangue et al. (2010). Temperature was controlled by placing culture mesocosms in baths containing seawater at 13°C or 18°C.
|
| Growth protocol |
Ferilized eggs were cultured under four different seawater pCO2 concentrations and temperatures: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. Larval cultures were performed as described in Fangue et al. (2010). A laboratory-based, experimental system for the study of ocean acidification effects on marine invertebrate larvae. Limnology and Oceanography: Methods 8: 441–452.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
200 ng of clean, total RNA from either experimental or reference samples were amplified and labeled with Cy5 or Cy3 fluorescent dyes, respectively, using Agilent's Low-Input Quick Amp Two Color Labeling Kit (#5190-2306, Agilent Technologies Inc., Santa Clara, CA, USA).
|
| |
|
| Channel 2 |
| Source name |
Total RNA pooled from aliquots of total RNA from all experimental samples and labeled with Cyanine-3 (green).
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
sample type: Reference
|
| Treatment protocol |
pCO2 within each culture was manipulated by bubbling CO2 gas into seawater as described in Fangue et al. (2010). Temperature was controlled by placing culture mesocosms in baths containing seawater at 13°C or 18°C.
|
| Growth protocol |
Ferilized eggs were cultured under four different seawater pCO2 concentrations and temperatures: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. Larval cultures were performed as described in Fangue et al. (2010). A laboratory-based, experimental system for the study of ocean acidification effects on marine invertebrate larvae. Limnology and Oceanography: Methods 8: 441–452.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
200 ng of clean, total RNA from either experimental or reference samples were amplified and labeled with Cy5 or Cy3 fluorescent dyes, respectively, using Agilent's Low-Input Quick Amp Two Color Labeling Kit (#5190-2306, Agilent Technologies Inc., Santa Clara, CA, USA).
|
| |
|
| |
| Hybridization protocol |
Amplified and labled RNA whose yield and specific activity exceeded 1.875 µg and 6 pmol, repsectively, were hybridized to each array according to instructions for Agilent's Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol.
|
| Scan protocol |
Scanned using an Axon GenePix 4000B microarray scanner, adjusting the PMT gain for optimized visualization of each slide.
|
| Description |
Biological replicate 1 of 3 from 13°C/1100 µatm sampled at pluteus stage
|
| Data processing |
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Only genes 2.6 times above background, but not saturated in all samples were analyzed. Different probes targeting the same gene loci (e.g. SPU) were summarized by computing the geometric mean.
|
| |
|
| Submission date |
Jul 05, 2012 |
| Last update date |
Jan 01, 2013 |
| Contact name |
Tyler G Evans |
| E-mail(s) |
tyler.evans@lifesci.ucsb.edu, tylergevans@gmail.com
|
| Phone |
8058936176
|
| Fax |
8058938062
|
| Organization name |
University of California Santa Barbara
|
| Department |
Ecology, Evolution and Marine Biology
|
| Lab |
Hofmann
|
| Street address |
Marine Science Institute
|
| City |
Santa Barbara |
| State/province |
California |
| ZIP/Postal code |
93106-9620 |
| Country |
USA |
| |
|
| Platform ID |
GPL15767 |
| Series (1) |
| GSE39125 |
Synergistic effects of temperature and pCO2 on growth, development and gene expression of Strongylocentrotus purpuratus larvae |
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