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Sample GSM337573 Query DataSets for GSM337573
Status Public on Oct 27, 2009
Title 3d, pineal, day, rep2
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 2 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 3061.6 P
AFFX-BioB-M_at 5547.7 P
AFFX-BioB-3_at 4189.2 P
AFFX-BioC-5_at 9045.9 P
AFFX-BioC-3_at 5253.4 P
AFFX-BioDn-5_at 13126.9 P
AFFX-BioDn-3_at 34536.3 P
AFFX-CreX-5_at 41653.3 P
AFFX-CreX-3_at 60448.3 P
AFFX-DapX-5_at 7.6 A
AFFX-DapX-M_at 34.4 A
AFFX-DapX-3_at 15.6 A
AFFX-LysX-5_at 38.3 A
AFFX-LysX-M_at 35.9 A
AFFX-LysX-3_at 33.4 A
AFFX-PheX-5_at 9.2 A
AFFX-PheX-M_at 16 A
AFFX-PheX-3_at 39.4 A
AFFX-ThrX-5_at 18.2 A
AFFX-ThrX-M_at 9.8 A

Total number of rows: 15617

Table truncated, full table size 369 Kbytes.




Supplementary file Size Download File type/resource
GSM337573.cel.gz 2.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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