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Sample GSM113855 Query DataSets for GSM113855
Status Public on Jan 25, 2007
Title Wild type retina, 52hpf, pool of ten tissues, biological replicate 2 WR_52hpf_rep2 (WR52_2)
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 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 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 105.2148004
AFFX-BioB-5_at 183.1364226
AFFX-BioB-M_at 185.5148078
AFFX-BioC-3_at 360.8880818
AFFX-BioC-5_at 332.0141091
AFFX-BioDn-3_at 1849.225572
AFFX-BioDn-5_at 893.8151079
AFFX-CreX-3_at 6970.252671
AFFX-CreX-5_at 3537.042465
AFFX-DapX-3_at 181.3956887
AFFX-DapX-5_at 14.58042647
AFFX-DapX-M_at 49.6752225
AFFX-Dr-AB076373-1_at 29.88509079
AFFX-Dr-acta1-3_at 127.4725385
AFFX-Dr-acta1-5_at 83.36975126
AFFX-Dr-acta1-5_x_at 132.8060931
AFFX-Dr-acta1-M_at 22.03814252
AFFX-Dr-AF292559-1_at 14.27986373
AFFX-Dr-AF292559-2_s_at 8.734152635
AFFX-Dr-AF292559-3_s_at 10.05981123

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM113855.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM113855.DAT.gz 39.1 Mb (ftp)(http) DAT
Raw data provided as supplementary file

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