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| Status |
Public on Jan 01, 2019 |
| Title |
Spring_ 1ug Ag_21d_4 |
| Sample type |
RNA |
| |
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| Source name |
Digestive gland_Spring_1ug Ag_21 days_org 4
|
| Organism |
Mytilus galloprovincialis |
| Characteristics |
gender: Female
size: 3.5-4.5 cm shell length
treatment: 21 days of dietary exposure to 1 ug/L of Ag NPs in spring
|
| Treatment protocol |
Mussels in the control tank were fed for 21 days with the microalgae Isochrysis galbana (20x106 cells/mussel·day) and mussels in the treatment tank were fed for 21 days with the same dose of microalgae I. galbana (20x106 cells/mussel·day) previously exposed for 24 hours to 1 μg Ag/L Ag NPs in spring or to 10 μg Ag/L Ag NPs in autumn and in spring. Water was renewed every day before animal feeding. After 1 and 21 days of exposure, digestive gland of mussels was dissected out, immersed in RNA later, snap-frozen in liquid nitrogen and stored at -80°C until processing.
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| Growth protocol |
Mussels Mytilus galloprovincialis 3.5-4.5 cm in shell length were collected in autumn (November 2013) and spring (March 2014) from San Felipe, Galicia (43° 27.599'N, 8° 17.904'W). Upon arrival to the laboratory, mussels were placed in an acclimation tank (temperature =15.6°C, salinity =28.7, conductivity =36.4 mS/cm, pH =7.7 at light regime 12 h/12 h L/D) for 5 days without feeding. Then mussels were fed with Isochrysis galbana microalgae (20x106 cells/mussel·day) for additional 5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
About 50-100 mg of digestive gland of 10 female mussels per treatment were individually homogenized in TRIzol® Reagent (Invitrogen, Carlsbad, USA) using a Precellys®24 homogenizer (Bertin Technologies, France) at a shaking speed of 6000 rpm for 2 cycles of 25 seconds each. Total RNA was isolated following the manufacturer´s recommendations and treated with the RNase-Free DNase Set (Qiagen, Venlo, The Netherlands) to digest contaminating DNA. Then, total RNA was purified by using the RNeasy Mini Kit (Qiagen). The integrity and quality of purified RNA was checked both spectrophotometrically (A260/280; Epoch Biotek; Winooski, Vermont, USA) and by capillary electrophoresis (Agilent 2100 Bioanalyzer, Agilent Technologies). Samples with a A260/280 ratio around 2 and showing a good electropherogram were selected for microarray hybridizations.
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| Label |
Cy3
|
| Label protocol |
RNA samples (100 ng) were retro-transcribed and labelled using the Low Input Quick Amp Labelling Kit, One Colour (Agilent Technologies, 5190-2305) following the manufacturer’s instructions.
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| |
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| Hybridization protocol |
Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 600 ng. Volume: 40 µL. Temperature (ºC): 65. Duration: 17 hours at 10 rpm in the hybridization oven. After hybridization, microarrays were washed following manufacturer´s instructions.
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| Scan protocol |
Hybridized microarrays were scanned on a G2565CA DNA microarray scanner (Agilent Technologies) with ozone barrier slide covers (Agilent Technologies P/N G2505-60550). Scan resolution: 3µm; Dye Channel: green
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| Description |
Gene expression after 21 days of dietary exposure to 1 µg/L of Ag NPs in spring
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| Data processing |
The scanned images were analyzed with Feature Extraction Software v.10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09, Design File: 078472_D_F_20150925) to obtain background subtracted and spatially detrended Processed Signal intensities.
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| |
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| Submission date |
Dec 19, 2018 |
| Last update date |
Jan 02, 2019 |
| Contact name |
Nerea Duroudier |
| Organization name |
University of the Basque Country
|
| Street address |
Bº Sarriena s/n
|
| City |
Leioa |
| ZIP/Postal code |
48940 |
| Country |
Spain |
| |
|
| Platform ID |
GPL25964 |
| Series (1) |
| GSE124126 |
Effects of PVP/PEI coated Ag nanoparticles on dietarily exposed mussels Mytilus galloprovincialis at different seasons: a transcriptomic study. |
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