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Sample GSM1054085 Query DataSets for GSM1054085
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).
 
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.
 
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

Data table header descriptions
ID_REF
VALUE normalized log10 ratio Cy5/Cy3

Data table
ID_REF VALUE
1 4.851484466e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 5.388790286e-002
13 -1.169357387e-001
14 9.828466511e-002
15 0.000000000e+000
16 -1.546338852e-001
17 -1.720995276e-002
18 2.634133579e-001
19 -5.608803958e-002
20 -7.146812084e-002

Total number of rows: 45220

Table truncated, full table size 1025 Kbytes.




Supplementary file Size Download File type/resource
GSM1054085_US22502677_252643710188_S01_GE2_105_Dec08_1_3.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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