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Sample GSM337580 Query DataSets for GSM337580
Status Public on Oct 27, 2009
Title 3d, pineal, night, rep3
Sample type RNA
Source name 3d old, pineal gland, night-time
Organism Danio rerio
Characteristics Embryo
Growth protocol Adults and embryos were kept at 28.5oC under a 14-hr-light/10-hr-dark cycle.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cDNA was prepared using the Ovation Biotin system kit (NeuGen) according to the manufacturer's instructions.
Hybridization protocol 2.2 micrograms of labeled cDNA was hybridized to the Affymetrix zebrafish GeneChip at 45 degrees C for 18 hrs. Post-hybridization, staining, and washing were performed using a Fluidics Station 450 (Affymetrix) with protocol EukGE-WS2v4_450.
Scan protocol The hybridized chips were scanned by Affymetrix GeneChip Scanner 3000 and then processed with GeneChip Operating Software (GCOS).
Description Biological replicate 3 of 4
Data processing Global scaling was employed for analysis and the target Intensity value (TGT) was set as 500 following the manufacturer's (Affymetrix) recommendations. GeneChip Operating Software (Affymetrix) was used to create CEL files from each experiment. Further statistical analysis was done using JMP, the statistical Discovery Software (
Submission date Oct 27, 2008
Last update date Oct 27, 2008
Contact name Reiko Toyama
Phone 301-496-9689
Fax 301-496-0243
Organization name NIH
Department NICHD
Lab Lab. of Molecular Genetics
Street address Bldg.6B, Room 420, 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL1319
Series (1)
GSE13371 Transcriptome analysis of the zebrafish pineal gland

Data table header descriptions
VALUE Signal calculated by GCOS1.2 software
ABS_CALL Call in an absolute analysis that indicates if the signal was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 5309.1 P
AFFX-BioB-M_at 9311.5 P
AFFX-BioB-3_at 7934.7 P
AFFX-BioC-5_at 17489.4 P
AFFX-BioC-3_at 10040.7 P
AFFX-BioDn-5_at 27121.4 P
AFFX-BioDn-3_at 58581.1 P
AFFX-CreX-5_at 78377.9 P
AFFX-CreX-3_at 121865.4 P
AFFX-DapX-5_at 4.1 A
AFFX-DapX-M_at 11.9 A
AFFX-DapX-3_at 35.9 A
AFFX-LysX-5_at 88.8 A
AFFX-LysX-M_at 20.2 A
AFFX-LysX-3_at 78.9 A
AFFX-PheX-5_at 5.9 A
AFFX-PheX-M_at 6.9 A
AFFX-PheX-3_at 8.1 A
AFFX-ThrX-5_at 4.8 A
AFFX-ThrX-M_at 22.8 A

Total number of rows: 15617

Table truncated, full table size 369 Kbytes.

Supplementary file Size Download File type/resource
GSM337580.cel.gz 1.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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