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Sample GSM1293346 Query DataSets for GSM1293346
Status Public on Feb 19, 2014
Title Brain-Young-Male-1
Sample type RNA
 
Source name young zebrafish, brain, male
Organism Danio rerio
Characteristics tissue: brain
strain: AB
Treatment protocol For the brain dissection, fish were anesthetized in Tricaine (Sigma-Aldrich, Germany) and head was separated from the body with a scalpel. The eyes/optic nerves were dissected, brain was dissected away from dorsal surface. Following visualization of the brain, it was removed from the skull. Tissues were weighed in 0.5 ml microtubes, frozen in liquid nitrogen and stored at -80°C until RNA isolation.
Growth protocol Fish were maintained at a constant temperature of 28°C on a 14L:10D light cycle. All the fish were fed three times daily and kept in a recirculating system at all times. All animals were kept in groups, around 10 animals in a 4L tank.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed with a RNAeasy Mini Kit (Qiagen, Germany). DNase treatment was done with RNase-free DNase Set (Qiagen, Germany).
Label Biotin
Label protocol RNA was amplified with Ovation RNA Amplification System (NuGen) and biotin-labeled with Encore Biotin Module (NuGen).
 
Hybridization protocol Affymetrix protocol
Scan protocol Affymetrix protocol
Description 8.5 month old male, fish no: HD38
Data processing Raw Affymetrix CEL files were processed with RMA normalization method. Probesets were annotated using BioMart (http://www.biomart.org/biomart/martview) with the current Zebrafish Genome Built (Danio rerio Zv9).
 
Submission date Dec 18, 2013
Last update date Feb 19, 2014
Contact name Ayca Arslan Ergul
E-mail(s) aycaergul@gmail.com
Organization name Bilkent University
Department UNAM
Street address Bilkent Üniversitesi UNAM
City ANKARA
State/province ÇANKAYA
ZIP/Postal code 06800
Country Turkey
 
Platform ID GPL1319
Series (1)
GSE53430 Expression data from young and old zebrafish brain.

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
AFFX-BioB-5_at 9.229114
AFFX-BioB-M_at 9.521818
AFFX-BioB-3_at 9.784412
AFFX-BioC-5_at 10.10762
AFFX-BioC-3_at 9.311543
AFFX-BioDn-5_at 10.86506
AFFX-BioDn-3_at 12.56709
AFFX-CreX-5_at 13.23496
AFFX-CreX-3_at 13.87689
AFFX-DapX-5_at 9.792156
AFFX-DapX-M_at 10.44704
AFFX-DapX-3_at 11.79748
AFFX-LysX-5_at 7.811759
AFFX-LysX-M_at 8.909482
AFFX-LysX-3_at 8.781189
AFFX-PheX-5_at 7.75754
AFFX-PheX-M_at 8.767759
AFFX-PheX-3_at 9.489819
AFFX-ThrX-5_at 8.893847
AFFX-ThrX-M_at 8.863951

Total number of rows: 15617

Table truncated, full table size 391 Kbytes.




Supplementary file Size Download File type/resource
GSM1293346_S0806F0001_H.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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