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| Status |
Public on Jun 13, 2017 |
| Title |
Enchytraeus crypticus_Ni-NPs EC20 3days_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Tissue: Whole body extracts (20 organisms), Stage of development: Adult organisms with well developed clitellum, Exposure: Ni-NPs EC20 (effect concentration on reproduction) in soil for 3 days
|
| Organism |
Enchytraeus crypticus |
| Characteristics |
tissue: Whole body extracts
stage of development: Adult organisms with well developed clitellum
treatment: Ni-NPs EC20 3days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using SV Total RNA Isolation System (Promega Corporation, USA).The quantity and purity of the RNA samples was checked using the ND-1000 spectrophotometer (Nanodrop®, USA) through measurement of the 260nm/280nm and 260nm/230nm absorbance. For all used samples these ratios were approximately 2. To verify the integrity of the RNA samples, a denaturating formaldehyde agarose gel electrophoresis was performed.
|
| Label |
Cy3
|
| Label protocol |
Labelling and hybridizations followed the protocol “One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling” from Agilent Technologies (Agilent Technologies, Palo Alto, CA, USA)). Briefly, 500 ng of total RNA was amplified and labelled with Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Palo Alto, CA, USA). Positive controls were added with the Agilent one-colour RNA Spike-In Kit (Agilent Technologies, Palo Alto, CA, USA). Purification of the amplified and labelled cRNA was performed with the RNeasy columns (Qiagen, Valencia, CA, USA).
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| Hybridization protocol |
The cRNA samples were hybridized on the Custom Gene Expression Agilent Microarrays (4 x 44k format) developed for Enchytraeus crypticus. Hybridizations were performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA, USA) and each biological replicate was individually hybridized on one array. The arrays were hybridized at 65ºC with a rotation of 10 rpm, during 17h. After that the microarrays were washed using Agilent Gene Expression Wash Buffer Kit (Agilent Technologies, Palo Alto, CA, USA)
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| Scan protocol |
Scanning was performed using the Agilent DNA microarray scanner G2505B (Agilent Technologies). Fluorescence intensity data was obtained with Feature Extraction (10.5.1.1) Software (Agilent Technologies).
|
| Data processing |
Background correction was provided by Agilent Feature Extraction software and only gene probes with good signal quality (flag IsPosAndSignif = True) in all samples were employed in the analyses.
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| |
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| Submission date |
Jun 11, 2015 |
| Last update date |
Jun 13, 2017 |
| Contact name |
Susana Isabel Lopes Gomes |
| E-mail(s) |
susana.gomes@ua.pt
|
| Organization name |
CESAM & University of Aveiro
|
| Department |
Biology
|
| Street address |
Campus Universitário de Santiago, Departement of Biology, University of Aveiro
|
| City |
Aveiro |
| ZIP/Postal code |
3810-193 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL20310 |
| Series (1) |
| GSE69793 |
Exposure to different nickel nanoparticles and nickel salt: gene expression profile in Enchytraeus crypticus |
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