|
| Status |
Public on Jan 30, 2018 |
| Title |
Embryos from eggs treated with DMSO (0.005%) |
| Sample type |
RNA |
| |
|
| Source name |
Embryos from eggs treated with DMSO
|
| Organism |
Danio rerio |
| Characteristics |
treatment: dimethyl sulfoxide (DMSO)
tissue: Embryos from eggs
|
| Treatment protocol |
Embryos were treated with chemical at 72-96 hours post fertilization and then sacrificed by removing water and quick-freezing on dry ice.
|
| Growth protocol |
Embryos were collected following natural spawning, washed, and 100 eggs were placed in 20 x 100 mm culture plates with 50 mL of egg water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA was used for biotin cRNA labeling according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Zebrafish Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
DMSO
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.7) and the Brainarray zebrafishdrentrezgcdf R package (version 14.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.download/Zebrafish_Dr_ENTREZG_14.0.0.zip).
|
| |
|
| Submission date |
Jan 29, 2018 |
| Last update date |
Jan 30, 2018 |
| Contact name |
Mara H. O'Brien |
| E-mail(s) |
toxdoc@yahoo.com
|
| Organization name |
University of Connecticut Health Center
|
| Department |
Craniofacial Sciences
|
| Street address |
263 Farmington Ave.
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24541 |
| Series (1) |
| GSE109826 |
Expression data from developing zebrafish embryos treated with pesticides and 11-ketotestosterone |
|
