|
| Status |
Public on Mar 07, 2015 |
| Title |
Control_rep4_exp2 vs. Nod_rep4_exp2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Nod rep4 exp2
|
| Organism |
Daphnia pulex |
| Characteristics |
Sex: female
developmental stage: adult
tissue: whole body
|
| Treatment protocol |
Animals were exposed for 10 days to a control diet or a diet containing 50% of one of the five cyanobacteria. Animals were fed daily and experimental jars were changed out three times a week. After 10 days RNA was extracted.
|
| Growth protocol |
4 day old animals were isolated from synchronized cultures of brood mothers. Mothers were fed a control diet of the non toxic green algae at an optimal diet ratio under constat light and temperature conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
|
| Label |
Cy3
|
| Label protocol |
cDNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.
|
| |
|
| Channel 2 |
| Source name |
Control rep4 exp2
|
| Organism |
Daphnia pulex |
| Characteristics |
Sex: female
developmental stage: adult
tissue: whole body
|
| Treatment protocol |
Animals were exposed for 10 days to a control diet or a diet containing 50% of one of the five cyanobacteria. Animals were fed daily and experimental jars were changed out three times a week. After 10 days RNA was extracted.
|
| Growth protocol |
4 day old animals were isolated from synchronized cultures of brood mothers. Mothers were fed a control diet of the non toxic green algae at an optimal diet ratio under constat light and temperature conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was homogenized and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
|
| Label |
Cy5
|
| Label protocol |
cDNA labeling using 1 O.D. Cy-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA.
|
| |
|
| |
| Hybridization protocol |
Labeled products were pooled and served as a final Master Mix for the array, The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate.
|
| Scan protocol |
Axon GenePix 4200 Professional, 5 micron resolution.
|
| Description |
Expression Analysis
|
| Data processing |
Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
|
| |
|
| Submission date |
Oct 28, 2014 |
| Last update date |
Mar 07, 2015 |
| Contact name |
Jana Asselman |
| E-mail(s) |
[email protected]
|
| Phone |
+32 9 264 37 64
|
| Organization name |
Ghent University
|
| Lab |
Laboratory of Environmental Toxicology and Aquatic Ecology
|
| Street address |
Coupure Links 653 (Building F, 2nd floor)
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL11278 |
| Series (1) |
| GSE62763 |
Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia |
|
