|
| Status |
Public on Jan 15, 2016 |
| Title |
D_T1T1 |
| Sample type |
RNA |
| |
|
| Source name |
Digestive_Gland_Sampling_Time1_Control
|
| Organism |
Magallana gigas |
| Characteristics |
tissue: Digestive_Gland
gender: Female
developmental stage: 1y
|
| Treatment protocol |
Polystyrene microplastic exposure at 32 µg.L-1
Gonadal maturation
|
| Growth protocol |
Standard hatchery conditions to induce gametogenesis (2 months at 17°C fed at libitum)
Standard hatchery conditions to induce gametogenesis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Extract-all Reagent (Eurobio), 1,5 mL per 50 mg of tissue or 20000 oocytes
Total RNA extracted using Extract-all Reagent (Eurobio), 1,5 mL per 50 mg of tissue
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color
200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color
|
| |
|
| Hybridization protocol |
Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA for 16 h at 65 °C
Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA, randomly onto 48 different slides for 16 h at 65 °C
|
| Scan protocol |
Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters
Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters
|
| Description |
Microarray_Gene_Expression
|
| Data processing |
Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.
Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.
|
| |
|
| Submission date |
Aug 07, 2015 |
| Last update date |
Jan 16, 2016 |
| Contact name |
Rossana Sussarellu |
| E-mail(s) |
rossana.sussarellu@ifremer.fr
|
| Organization name |
Ifremer
|
| Department |
Ressources Biologiques et Environnement
|
| Lab |
Laboratoire d'Ecotoxicologie
|
| Street address |
Rue de l'Ile d'Yeu
|
| City |
Nantes |
| ZIP/Postal code |
44300 |
| Country |
France |
| |
|
| Platform ID |
GPL11353 |
| Series (1) |
| GSE71845 |
Oyster reproduction is affected by exposure to polystyrene microplastics |
|
