|
| Status |
Public on Dec 01, 2022 |
| Title |
Brain_DA_treated_168_hour_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Brain, DA treated, 168 hour
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Analysis was done on three RNA replicates per time point, each consisting of RNA from 3-4 pooled brains. Total RNA was isolated from zebrafish brains using the miRNeasy Mini Kit (Qiagen Inc., Valencia, CA) following manufacturer’s instructions, and stored at -70°C. RNA quantity and quality (OD260/280 and OD260/230 ratios) were determined using a NanoDrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA integrity was characterized using the Agilent RNA 6000 Nano Kit with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
biotin
|
| Label protocol |
RNA was processed for hybridization to Affymetrix Zebrafish Genome array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
The standard hybridization protocol was used as recommended by Affymetrix
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health.
|
| Data processing |
Bioconductor oligo package, RMA normalization. Comparisons were made using the Bioconductor limma package, fitting an ANOVA model as well as an ANCOVA model with a 3 degree of freedom spline.
|
| |
|
| Submission date |
Jun 19, 2020 |
| Last update date |
Dec 01, 2022 |
| Contact name |
James William MacDonald |
| E-mail(s) |
jmacdon@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Environmental and Occupational Health Sciences
|
| Street address |
4225 Roosevelt Way NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105-6099 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE152814 |
Symptomatic Domoic Acid exposure in zebrafish |
|
