NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM113858 Query DataSets for GSM113858
Status Public on Jan 25, 2007
Title Wild type retina with retinal pigment epithelium attached, 52hpf, pool of 10 tiss, bio rep 2 WRR_52hpf_rep2 (WRR52_3)
Sample type RNA
 
Source name Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues
Organism Danio rerio
Characteristics Strain: AB
Genotype: Wild-type
Age: 52hpf
Tissue: Retina with Retinal pigment epithelium attached
Biomaterial provider Yuk Fai Leung/John E. Dowling
Treatment protocol Ten tissues were dissected from developing embryos according to: Leung YF, Ma P, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retinal Pigment Epithelium in vivo. 2007;48:881-890., and pooled as one biological replicate.
Growth protocol Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.
Label Biotin
Label protocol Thirty-three nanograms of total RNA were labeled by Affymetrix GeneChip Two-Cycle Target Labeling protocol.
 
Hybridization protocol Hybridization, washing and staining were done according to a standard procedure from Affymetrix.
Scan protocol Scanning was done according to a standard procedure from Affymetrix.
Description Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 2
Data processing The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.
 
Submission date Jun 11, 2006
Last update date Aug 24, 2007
Contact name Yuk Fai Leung
E-mail(s) yfleung@purdue.edu
Phone 765-496-3153
Organization name Purdue University
Department Biological Sciences
Lab Leung
Street address 915 W. State Street
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL1319
Series (1)
GSE5048 Gene Expression Profiling of Zebrafish Embryonic Retinal Pigment Epithelium in vivo.

Data table header descriptions
ID_REF
VALUE The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7, running in the R statistical environment version 2.2.0 using default parameters.

Data table
ID_REF VALUE
AFFX-BioB-3_at 131.0679783
AFFX-BioB-5_at 196.512329
AFFX-BioB-M_at 151.2488943
AFFX-BioC-3_at 340.5331321
AFFX-BioC-5_at 402.7876634
AFFX-BioDn-3_at 2027.206022
AFFX-BioDn-5_at 930.3626745
AFFX-CreX-3_at 6179.902433
AFFX-CreX-5_at 3584.489958
AFFX-DapX-3_at 470.1141035
AFFX-DapX-5_at 15.32935063
AFFX-DapX-M_at 113.1791369
AFFX-Dr-AB076373-1_at 24.19684265
AFFX-Dr-acta1-3_at 179.2608215
AFFX-Dr-acta1-5_at 108.1356617
AFFX-Dr-acta1-5_x_at 159.9375105
AFFX-Dr-acta1-M_at 23.9331899
AFFX-Dr-AF292559-1_at 13.17225326
AFFX-Dr-AF292559-2_s_at 9.870362949
AFFX-Dr-AF292559-3_s_at 11.81236721

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM113858.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM113858.DAT.gz 37.6 Mb (ftp)(http) DAT
Raw data provided as supplementary file

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