NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM337594 Query DataSets for GSM337594
Status Public on Oct 27, 2009
Title 5d, pineal, night, rep1
Sample type RNA
 
Source name 5d 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 1 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 (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 1238.7 P
AFFX-BioB-M_at 2264.5 P
AFFX-BioB-3_at 1690 P
AFFX-BioC-5_at 3486.3 P
AFFX-BioC-3_at 1470.7 P
AFFX-BioDn-5_at 2426 P
AFFX-BioDn-3_at 12192.2 P
AFFX-CreX-5_at 26001.2 P
AFFX-CreX-3_at 35224.9 P
AFFX-DapX-5_at 5.2 A
AFFX-DapX-M_at 7 A
AFFX-DapX-3_at 13 A
AFFX-LysX-5_at 3.9 A
AFFX-LysX-M_at 9.9 A
AFFX-LysX-3_at 7.4 A
AFFX-PheX-5_at 9.7 A
AFFX-PheX-M_at 38.5 A
AFFX-PheX-3_at 11.3 A
AFFX-ThrX-5_at 5.6 A
AFFX-ThrX-M_at 22.3 A

Total number of rows: 15617

Table truncated, full table size 368 Kbytes.




Supplementary file Size Download File type/resource
GSM337594.cel.gz 1.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap