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Sample GSM333307 Query DataSets for GSM333307
Status Public on May 01, 2009
Title Pineal_DD_ZT18
Sample type RNA
 
Source name pineal at ZT18, constant darkness
Organism Danio rerio
Characteristics Tg(aanat2:EGFP)Y8 transgenic zebrafish
Age: adult (3-6 months)
Gender: males and females
Treatment protocol Fish were anesthetized in 1.5 mM Tricane (Sigma) and sacrificed by decapitation, and pineal glands were removed under a fluorescent dissecting microscope. 12 pineal glands were collected and pooled at each time point and at each light condition.
Growth protocol Adult zebrafish were raised in a light- and temperature-controlled recirculation water system under a 12-h light/12-h dark cycle at 28 ┬░C and fed twice a day.
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, Qiagen).
Label biotin
Label protocol Double-strand cDNA was generated from 10-100 ng of mRNA by using a T7-linked oligo(dT) primer (Affymetrix). After second-strand synthesis, in vitro transcription was performed with MEGAscript® T7 Kit (Ambion, Inc.). The cRNA (600ng) was then used for second cycle first-strand cDNA (Affymetrix) by using a T7-linked oligo(dT) primer (Affymetrix). After 2nd cycle - second-strand synthesis, in vitro transcription was again performed; this time biotinylated UTP and CTP (Affymetrix) were incorporated in the cRNA, resulting in approximately 1800-fold amplification of labeled RNA.
 
Hybridization protocol The target cRNA generated from each sample was fragmented and 15 micogram of the fragmented cRNA was added to the hybridization cocktail which includes in addition to the fragmented target, probe array controls (pre-mixed biotin-labeled bioB, bioC, bioD and cre, in staggered concentrations, ready to be added directly to the hybridization cocktail. These controls facilitate monitoring of the hybridization process for troubleshooting), BSA, and herring sperm DNA. It was then hybridized to the probe array during a 16-hour incubation at 45 deg (C). The array was then washed and stained on the Affymetrix fluidic station (using Streptavidin-Phycoerythrin which binds to the biotinylated UTP and CTP incorporated previously in the hybridized cRNA).
Scan protocol The stained array was scanned on the Affymetrix scanner (450).
Description Gene expression data from zebrafish pineal
Data processing The GCOS (Gene Operating System) generates the numerical data from the scanned intensities using the MAS 5 software (MicroArray suite 5.0; Affymetrix).
 
Submission date Oct 14, 2008
Last update date Oct 14, 2008
Contact name Yoav Gothilf
E-mail(s) YoavG@tauex.tau.ac.il
Phone +972-3-640-6329
Fax +972-3-640-6329
Organization name Tel Aviv University
Department Neurobiology, Faculty of Life Sciences
Lab Gothilf
Street address Sherman Building, Room 405
City Tel Aviv
ZIP/Postal code 69978
Country Israel
 
Platform ID GPL1319
Series (1)
GSE13196 Expression data from zebrafish pineal gland

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity

Data table
ID_REF VALUE
Dr.9890.1.A1_at 5940.9
Dr.14317.1.A1_at 1379.4
AFFX-DapX-3_at 2547.6
Dr.12469.1.S1_at 3784
Dr.9901.1.S1_at 1451.9
Dr.9841.1.A1_at 5333.7
AFFX-r2-Bs-dap-3_at 1973.7
Dr.9908.1.A1_at 6803.7
Dr.12466.1.A1_s_at 3596.4
Dr.11215.1.A1_at 7587.2
Dr.14325.1.S1_at 1233.1
AFFX-r2-Bs-dap-M_at 729.2
Dr.8142.1.S1_at 9780.1
Dr.12451.2.A1_at 3737.3
Dr.20055.1.A1_at 6530.7
Dr.11072.1.A1_at 691.8
Dr.23415.1.A1_at 6764.8
Dr.12592.1.S1_at 1336.5
Dr.11183.1.A1_at 3539.1
Dr.9899.1.S2_at 5063.8

Total number of rows: 15617

Table truncated, full table size 331 Kbytes.




Supplementary file Size Download File type/resource
GSM333307.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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