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Sample GSM113854 Query DataSets for GSM113854
Status Public on Jan 25, 2007
Title Wild type retina, 52hpf, pool of ten tissues, biological replicate 1 WR_52hpf_rep1 (WR52_1)
Sample type RNA
 
Source name Wild type retina, 52hpf, pool of ten tissues
Organism Danio rerio
Characteristics Strain: AB
Genotype: Wild-type
Age: 52hpf
Tissue: Retina
Biomaterial provider Yuk Fai Leung/John E. Dowling
Treatment protocol Ten tissues were dissected from developing embryos according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283., 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, 52hpf, pool of ten tissues, biological replicate 1
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 Jan 25, 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 219.3033016
AFFX-BioB-5_at 326.794555
AFFX-BioB-M_at 341.1823454
AFFX-BioC-3_at 673.9104915
AFFX-BioC-5_at 660.4345766
AFFX-BioDn-3_at 3068.776442
AFFX-BioDn-5_at 1749.193501
AFFX-CreX-3_at 11431.08063
AFFX-CreX-5_at 6253.46076
AFFX-DapX-3_at 87.77483803
AFFX-DapX-5_at 15.70174977
AFFX-DapX-M_at 39.42869792
AFFX-Dr-AB076373-1_at 24.00715236
AFFX-Dr-acta1-3_at 102.4597103
AFFX-Dr-acta1-5_at 85.45816664
AFFX-Dr-acta1-5_x_at 131.3249253
AFFX-Dr-acta1-M_at 33.62239596
AFFX-Dr-AF292559-1_at 13.5169525
AFFX-Dr-AF292559-2_s_at 8.44588616
AFFX-Dr-AF292559-3_s_at 10.22836732

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM113854.CEL.gz 3.3 Mb (ftp)(http) CEL
GSM113854.DAT.gz 36.8 Mb (ftp)(http) DAT
Raw data provided as supplementary file

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