|
Status |
Public on Jul 17, 2014 |
Title |
Zebrafish Control Cy3-Trained Cy5 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
control pooled whole zebrafish larvae
|
Organism |
Danio rerio |
Characteristics |
age: 10 days post fertilization tissue: whole zebrafish larva treatment: control strain: wild type zebrafish genetic background: Wageningen wild type X Tubingen wildtype (Zod2)
|
Treatment protocol |
Wildtype zebrafish were subjected to swim-training from 5 until 10 dpf (each day in sessions of three hours from 8:30-18:30). Fish were sampled at 10 dpf, at the end of the day, and frozen in liquid nitrogen and stored at -80°C until further use.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from each individual fish was isolated with the Qiagen Rneasy kit according to the manufacturer's protocol (Qiagen, Hilden, Germany)
|
Label |
Cy3
|
Label protocol |
Equal amounts RNA (400 ng) of 10 individual fish was pooled (trained/control). Subsequently, 100 ng of pooled RNA (control/trained) was labeled with Cy5 and Cy3. Equal amounts of labeled RNA of the pooled control samples were mixed with the labeled RNA of the trained samples (Control-Cy3 with Trained-Cy5 and Control-Cy5 with Trained-Cy3). Labeling of total RNA was performed according to the manufacturer's protocol (Two-color Microarray-based gene expression analysis, version 6.0, low input quick amp labeling, Agilent Technologies, Palo Alto, USA).
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|
|
Channel 2 |
Source name |
trained pooled whole zebrafish larvae
|
Organism |
Danio rerio |
Characteristics |
treatment: swim training age: 10 days post fertilization tissue: whole zebrafish larva strain: wild type zebrafish genetic background: Wageningen wild type X Tubingen wildtype (Zod2)
|
Treatment protocol |
Wildtype zebrafish were subjected to swim-training from 5 until 10 dpf (each day in sessions of three hours from 8:30-18:30). Fish were sampled at 10 dpf, at the end of the day, and frozen in liquid nitrogen and stored at -80°C until further use.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA from each individual fish was isolated with the Qiagen Rneasy kit according to the manufacturer's protocol (Qiagen, Hilden, Germany)
|
Label |
Cy5
|
Label protocol |
Equal amounts RNA (400 ng) of 10 individual fish was pooled (trained/control). Subsequently, 100 ng of pooled RNA (control/trained) was labeled with Cy5 and Cy3. Equal amounts of labeled RNA of the pooled control samples were mixed with the labeled RNA of the trained samples (Control-Cy3 with Trained-Cy5 and Control-Cy5 with Trained-Cy3). Labeling of total RNA was performed according to the manufacturer's protocol (Two-color Microarray-based gene expression analysis, version 6.0, low input quick amp labeling, Agilent Technologies, Palo Alto, USA).
|
|
|
|
Hybridization protocol |
Control-Cy3 with Trained-Cy5 and Control-Cy5 with Trained-Cy3 were hybridized on 4x44k Zebrafish Agilent microarrays and placed in a hybridization chamber at 10 rpm for maximum 17 hours at 65°C. After hybridization, slides were washed and mounted.
|
Scan protocol |
Slides were scanned on a Agilent Scanner 22502677
|
Description |
control (labeled with Cy3) and trained (labeled with Cy5) samples hybridized together on one array
|
Data processing |
Data was extracted with Agilent Feature Extraction Software (Version 10.5.1.1) and used for background subtraction and normalization.
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|
|
Submission date |
Dec 17, 2012 |
Last update date |
Jul 18, 2014 |
Contact name |
ansa fiaz |
E-mail(s) |
ansa.wasim@gmail.com
|
Organization name |
Wageningen University
|
Street address |
De Elst 1
|
City |
Wageningen |
ZIP/Postal code |
6708 WD |
Country |
Netherlands |
|
|
Platform ID |
GPL14688 |
Series (1) |
GSE42967 |
Wild-type Zebrafish subjected to swim-training |
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