|
| Status |
Public on Feb 01, 2017 |
| Title |
DMSO_rep_2_batch_3_arraySlide_10 |
| Sample type |
RNA |
| |
|
| Source name |
Whole embryo_48 hpf_DMSO
|
| Organism |
Danio rerio |
| Characteristics |
tissue: whole embryo
treatment: DMSO
|
| Treatment protocol |
Dechorionated embryos were nominally exposed to statis aqueous concentrations of each chemical or vehicle control (maximum DMSO was 0.64% for all exposures) from 6-48 hpf. Embryos were maintained at 28 °C throughout exposure
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was exctracted using the Quick-RNA MiniPrep kit (Zymo Research, Irvine, CA) according to manufacturer's protocols with the optional Dnase I digestion. Whole embryos were homogenized in 300 uL lysis buffer with 0.5 mm zirconium oxide beads using a bullet blender (Next Advance, Averill Park, NY) for 3 min at speed 8.
|
| Label |
Cy3
|
| Label protocol |
0.5 ug of Cy3-labeled cRNA was generated using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Santa Clara, CA)
|
| |
|
| Hybridization protocol |
Samples were hybridized to OakLabs ArrayXS Zebrafish microarrays using the Gene Experssion Hybridization Kit (Agilent)
|
| Scan protocol |
Slides were scanned after hybridization using the SureScan Microarray Scanner (Agilent)
|
| Description |
Gene expression after 48 hpf exposure
SG12414235_256950710033_S001_GE1_1105_Oct12_2_3
|
| Data processing |
Scanned images were read and processed using Agilent Feature Extraction software (ver 11) and analzed using limma in R. Data were background corrected using the MLE method and then quantile normalized. Prior to linear modeling and differential expression calculation, control probes and any probe that was less than 10% brighter than the negative control probes on at least four of the arrays were excluded from the analysis. Data preprocessing also showed batch effects due to array slide. We corrected for thi batch effect using the ComBat algorithm prior to linear modeling. The following arrays were removed from analysis due to outlier detection: SG12414235_256950710038_S001_GE1_1105_Oct12_2_2.txt, SG12414235_256950710027_S001_GE1_1105_Oct12_1_4.txt, SG12414235_256950710030_S001_GE1_1105_Oct12_1_2.txt, SG12414235_256950710023_S001_GE1_1105_Oct12_2_4.txt, SG12414235_256950710029_S001_GE1_1105_Oct12_2_4.txt, SG12414235_256950710023_S001_GE1_1105_Oct12_2_2.txt, SG12414235_256950710025_S001_GE1_1105_Oct12_1_3.txt, SG12414235_256950710039_S001_GE1_1105_Oct12_2_3.txt, SG12414235_256950710029_S001_GE1_1105_Oct12_1_1.txt
|
| |
|
| Submission date |
Nov 11, 2016 |
| Last update date |
Feb 01, 2017 |
| Contact name |
Robert L Tanguay |
| E-mail(s) |
robert.tanguay@oregonstate.edu
|
| Phone |
541-737-6514
|
| Organization name |
Oregon State University
|
| Department |
EMT
|
| Street address |
1007 ALS
|
| City |
Corvallis |
| State/province |
OR |
| ZIP/Postal code |
97331 |
| Country |
USA |
| |
|
| Platform ID |
GPL20686 |
| Series (1) |
| GSE89780 |
Classifying chemical endocrine activity using transcriptome profiling in zebrafish |
|
