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Sample GSM113856 Query DataSets for GSM113856
Status Public on Jan 25, 2007
Title Wild type retina, 52hpf, pool of ten tissues, biological replicate 3 WR_52hpf_rep3 (WR52_3)
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 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 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 86.8062362
AFFX-BioB-5_at 131.1329669
AFFX-BioB-M_at 131.1112058
AFFX-BioC-3_at 273.5941398
AFFX-BioC-5_at 278.0942593
AFFX-BioDn-3_at 1605.23432
AFFX-BioDn-5_at 713.6768587
AFFX-CreX-3_at 7123.752075
AFFX-CreX-5_at 3429.291396
AFFX-DapX-3_at 156.3062809
AFFX-DapX-5_at 13.49106554
AFFX-DapX-M_at 57.94237721
AFFX-Dr-AB076373-1_at 25.04981813
AFFX-Dr-acta1-3_at 117.7473101
AFFX-Dr-acta1-5_at 91.26206586
AFFX-Dr-acta1-5_x_at 155.8447336
AFFX-Dr-acta1-M_at 25.61845415
AFFX-Dr-AF292559-1_at 12.83668004
AFFX-Dr-AF292559-2_s_at 8.355283811
AFFX-Dr-AF292559-3_s_at 11.32486916

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM113856.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM113856.DAT.gz 38.1 Mb (ftp)(http) DAT
Raw data provided as supplementary file

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