Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 59
Release date: Jan 15 2016
Last update date: Apr 1 2016
Access: Public
Chemicals: Polystyrenes
Dataset link Oyster reproduction is affected by exposure to polystyrene microplastics

Experimental Protocol


To assess the impact of polystyrene microspheres (PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 32 µg L-1) for two months during a reproductive cycle and compared to control oysters. Adults were sampled 2 and 8 weeks after the beginning of exposure (corresponding to T1 and T3, respectively, 8-9 replicates per time of sampling and condition for a total of 56). Tissues were immediately dissected from each oyster, frozen in liquid nitrogen, then crushed to a fine powder at -196°C with an oscillating mill mixer and stored in liquid nitrogen until RNA extraction. Oocytes were collected from 5 females per condition, filtered in a 40 µm sieve, counted and transferred into 1.5 mL of Extract-all reagent (Eurobio, Courtaboeuf, France) (20,000 oocytes). Total RNA was isolated using 1.5 mL of Extract-all Reagent per 50 mg of gonad powder. For microarray hybridizations, 200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color. 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. The employed arrays were Agilent 60-mer 4x44K custom microarrays, containing 31,918 C. gigas ESTs, designed by Dheilly et al. (2011). Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters. Features were extracted using the Agilent Feature Extraction software 6.1.

Repositories


GEO

GSE71845

ArrayExpress

E-GEOD-71845

BioProject

PRJNA292304

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Contact


Rossana Sussarellu