|
| Status |
Public on Mar 02, 2016 |
| Title |
Female ovaries_5-6mpf_3 ppb_replicate 5 |
| Sample type |
RNA |
| |
|
| Source name |
Female ovaries, 3 ppb, replicate 5
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
genotype: wildtype
gender: Female
tissue: Ovaries
age: 5-6 mpf
|
| Treatment protocol |
Embryos were dosed with 0, 0.3, 3, or 30 ppb atrazine (CAS #1912-24-9; Chem Service, 98% purity) from 1-72 hours post fertilization (hpf) as previously described (Weber et al. 2013; Wirbisky et al., 2015). After the exposure, larvae were rinsed with clean fish system water, housed in 4-liter tanks in the system with 20-30 fish per tank, and allowed to mature under normal growing conditions.
|
| Growth protocol |
Zebrafish (wild-type AB strain) were housed in a Z-Mod System (Aquatic Habitats, Apopka, FL) on a 14:10 hour light:dark cycle and maintained at 28ºC ± 1°C with a pH of 7.0-7.2 and conductivity range of 470-520 µS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (ovarian tissue) was isolated by the RNeasy Mini Kit (Qiagen, Venlo, Limburg).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low Input QuickAmp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55mL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent custom zebrafish 4X180K Microarrays (060509) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Arrays were scanned on an Agilent Technologies SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA).
|
| Description |
Gene expression 5-6 mpf following embryonic atrazine exposure
|
| Data processing |
Array image data was extracted using Agilent Feature Extraction Software 11.5 (Agilent Technologies, Santa Clara, CA). Array image data was then uploaded to GeneSpring 12.5 (Agilent Technologies, Santa Clara, CA) for statistical analysis. Each gene list was imported into Ingenuity Pathway Analysis (IPA) for gene ontology and molecular pathway analysis.
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| |
|
| Submission date |
Oct 05, 2015 |
| Last update date |
Aug 11, 2022 |
| Contact name |
Jennifer Freeman |
| E-mail(s) |
[email protected]
|
| Organization name |
Purdue University
|
| Department |
School of Health Sciences
|
| Street address |
550 Stadium Mall Drive
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL20834 |
| Series (1) |
| GSE73740 |
An embryonic atrazine exposure results in reproductive dysfunction in adult zebrafish and morphological alterations in their offspring |
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