|
| Status |
Public on Jun 23, 2011 |
| Title |
LAAP_CON-4 |
| Sample type |
RNA |
| |
|
| Source name |
LAAP Exposure, Control treatment, 24h, replicate 4
|
| Organism |
Daphnia magna |
| Characteristics |
tissue: whole organism
sample type: control
|
| Treatment protocol |
Acetone was used as solvent carrier. Exposures were done with moderately hard-reconstituted water. An equivalent volume of clean acetone (≤ 1 mL/L) was spiked into control medium to ensure acetone did not confound results.
|
| Growth protocol |
Exposures were conducted in quadruplicated 1L glass beakers containing 750 ml of exposure water and 60 D. magna (6-8 days old) for 24 hours at 24 ± 1°C using a 16:8 photoperiod. The LAAP exposure was conducted using five replicates containing 115 D. magna each to increase statistical power. At the conclusion of each exposure, D. magna in each replicate and exposure were counted, weighed and flash-frozen then stored at -80oC until needed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy kits (Qiagen, Valencia, CA, USA). RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Wilmington, DE, USA) and quantity was determined using a Nanodrop® ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Total RNA was stored at -80oC until analyzed.
|
| Label |
Cy3
|
| Label protocol |
cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling kit; Agilent, Palo Alto, CA).
|
| |
|
| Hybridization protocol |
The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.
|
| Scan protocol |
An Agilent G2565CA Scanner (Agilent Technologies, Palo Alto, CA) was used to scan microarray images.
|
| Description |
Gene expression after 24h exposure to control water
|
| Data processing |
Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.
|
| |
|
| Submission date |
Jun 22, 2011 |
| Last update date |
Jun 23, 2011 |
| Contact name |
Natalia Vinas |
| E-mail(s) |
natalia@icnanotox.org, nataliarv@gmail.com
|
| Phone |
6016343764
|
| Organization name |
Mississippi State University
|
| Street address |
3909 Halls Ferry Rd
|
| City |
Vicksburg |
| State/province |
MS |
| ZIP/Postal code |
39180 |
| Country |
USA |
| |
|
| Platform ID |
GPL13761 |
| Series (1) |
| GSE30163 |
Assessment of chemical mixtures and ground water effects on Daphnia magna transcriptomics |
|
