|
Status |
Public on Mar 07, 2015 |
Title |
Control_rep2_exp1 vs. Ana_rep2_exp1 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Ana rep2 exp1
|
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 rep2 exp1
|
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) |
jana.asselman@ugent.be
|
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 |
|