|
| Status |
Public on Nov 17, 2011 |
| Title |
C_UV120h |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C1t0, C2t0, C3t0
|
| Organism |
Anemonia viridis |
| Characteristics |
tissue: tentacle (ectoderm+endoderm)
time: 0h (reference)
stress: UV stress (+1.25 mW.cm-2)
|
| Treatment protocol |
Anemonia viridis specimens were collected from Antibes, France. After 30 days of acclimation, sea anemones were subjected to a temperature stress (+10°C) or/and a UV stress (+1.25mW.cm-2) and a time course sampling was done over a 5 days period: T0 (reference), T24h, T48h and T120h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole tentacles was extracted using Trizol® Reagent (Invitrogen) following Chomczynski and Mackey procedure (BioTechniques, 1995). RNA was subjected to a DNase treatment (RQ1-DNAse, Promega), then resuspended in nuclease-free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and a Bioanalyzer 2100 (Agilent Technology), respectively.
|
| Label |
Cy5,Cy3
|
| Label protocol |
5µg of total RNA was labeled using the ChipShotTM Direct labeling system and further purified using the Clean-up system (Promega), according to the manufacturer's instructions. 5ng of a Lux mRNA exogenous standard was added to each sample before labeling.
|
| |
|
| Channel 2 |
| Source name |
C1t120, C2t120, C3t120
|
| Organism |
Anemonia viridis |
| Characteristics |
tissue: tentacle (ectoderm+endoderm)
time: 120h
stress: UV stress (+1.25 mW.cm-2)
|
| Treatment protocol |
Anemonia viridis specimens were collected from Antibes, France. After 30 days of acclimation, sea anemones were subjected to a temperature stress (+10°C) or/and a UV stress (+1.25mW.cm-2) and a time course sampling was done over a 5 days period: T0 (reference), T24h, T48h and T120h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole tentacles was extracted using Trizol® Reagent (Invitrogen) following Chomczynski and Mackey procedure (BioTechniques, 1995). RNA was subjected to a DNase treatment (RQ1-DNAse, Promega), then resuspended in nuclease-free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer and a Bioanalyzer 2100 (Agilent Technology), respectively.
|
| Label |
Cy5,Cy3
|
| Label protocol |
5µg of total RNA was labeled using the ChipShotTM Direct labeling system and further purified using the Clean-up system (Promega), according to the manufacturer's instructions. 5ng of a Lux mRNA exogenous standard was added to each sample before labeling.
|
| |
|
| |
| Hybridization protocol |
500 ng of each labeled cDNA was diluted in Hi-RPM Gene Expression Hyb buffer (Agilent) and hybridized on the array overnight at 47°C. Dye-swapping hybridizations were performed between the reference and each kinetic point (T0-Txh), for each sample (3 biological replicates) and condition (control, T°, UV, T°+UV).
|
| Scan protocol |
Slides were scanned using an AXON 4000B scanner (Molecular Devices). Image acquisition and quality control was performed using GenePix ® Pro 6.0 software.
|
| Description |
Raw file_Rep1: C1t0_C1t120.gpr
Raw file_Rep1: C1t120_C1t0.gpr
Raw file_Rep2: C2t0_C2t120.gpr
Raw file_Rep2: C2t120_C2t0.gpr
Raw file_Rep3: C3t0_C3t120.gpr
Raw file_Rep3: C3t120_C3t0.gpr
|
| Data processing |
Analyses were carried out using the LimmaGUI package for the R system. Normexp + offset (positive offset of 50) method was performed as background correction. Print-tip loess normalization was performed for each slide. Quantile normalisation was applied to mean-log intensities in order to make the distributions essentially equivalent across arrays.
|
| |
|
| Submission date |
Apr 12, 2011 |
| Last update date |
Nov 17, 2011 |
| Contact name |
Cecile Sabourault |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nice
|
| Department |
Biology
|
| Lab |
UMR7138
|
| Street address |
Faculte des Sciences, Parc Valrose, BP 71
|
| City |
NICE |
| ZIP/Postal code |
06108 |
| Country |
France |
| |
|
| Platform ID |
GPL10546 |
| Series (2) |
| GSE28566 |
Effects of UV and temperature on gene expression in the snakelocks sea anemone |
| GSE28577 |
Effects of UV and temperature stress on snakelocks sea anemone: ectoderm and endoderm |
|
