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Sample GSM337574 Query DataSets for GSM337574
Status Public on Oct 27, 2009
Title 3d, pineal, day, rep3
Sample type RNA
 
Source name 3d old, pineal gland, day-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 3
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 (http://www.jmp.com).
 
Submission date Oct 27, 2008
Last update date Oct 27, 2008
Contact name Reiko Toyama
E-mail(s) toyamar@mail.nih.gov
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
ID_REF
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
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 3153.5 P
AFFX-BioB-M_at 6178 P
AFFX-BioB-3_at 4704.3 P
AFFX-BioC-5_at 9725.6 P
AFFX-BioC-3_at 4262.2 P
AFFX-BioDn-5_at 9433.7 P
AFFX-BioDn-3_at 26980.5 P
AFFX-CreX-5_at 34821.2 P
AFFX-CreX-3_at 59922.2 P
AFFX-DapX-5_at 13.4 A
AFFX-DapX-M_at 7.1 A
AFFX-DapX-3_at 117.3 A
AFFX-LysX-5_at 75.9 A
AFFX-LysX-M_at 39.8 A
AFFX-LysX-3_at 22.4 A
AFFX-PheX-5_at 4.7 A
AFFX-PheX-M_at 43.7 A
AFFX-PheX-3_at 8.2 A
AFFX-ThrX-5_at 22.3 A
AFFX-ThrX-M_at 21.5 A

Total number of rows: 15617

Table truncated, full table size 369 Kbytes.




Supplementary file Size Download File type/resource
GSM337574.cel.gz 3.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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