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Sample GSM113859 Query DataSets for GSM113859
Status Public on Jan 25, 2007
Title Wild type retina with retinal pigment epithelium attached, 52hpf, pool of 10 tiss, bio rep 3 WRR_52hpf_rep3 (WRR52_4)
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 3
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 130.6206143
AFFX-BioB-5_at 166.9482504
AFFX-BioB-M_at 171.4015064
AFFX-BioC-3_at 396.34192
AFFX-BioC-5_at 434.9095758
AFFX-BioDn-3_at 2056.713654
AFFX-BioDn-5_at 874.1744087
AFFX-CreX-3_at 7246.309206
AFFX-CreX-5_at 3883.917151
AFFX-DapX-3_at 480.8924831
AFFX-DapX-5_at 17.33868636
AFFX-DapX-M_at 119.9432299
AFFX-Dr-AB076373-1_at 23.26732482
AFFX-Dr-acta1-3_at 164.9156913
AFFX-Dr-acta1-5_at 107.9136662
AFFX-Dr-acta1-5_x_at 159.6332615
AFFX-Dr-acta1-M_at 22.52877973
AFFX-Dr-AF292559-1_at 13.20442881
AFFX-Dr-AF292559-2_s_at 9.842617755
AFFX-Dr-AF292559-3_s_at 12.22003896

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM113859.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM113859.DAT.gz 37.2 Mb (ftp)(http) DAT
Raw data provided as supplementary file

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