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Sample GSM224828 Query DataSets for GSM224828
Status Public on Aug 04, 2008
Title YR_36hpf_rep2 (YR36_7-2)
Sample type RNA
 
Source name Young mutant retina, 36hpf, pool of twenty tissues
Organism Danio rerio
Characteristics Strain: AB
Genotype: young
Age: 36hpf
Tissue: Retina
Biomaterial provider Yuk Fai Leung/John E. Dowling
Treatment protocol Twenty 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. The young mutants were staged by staging their wild-type siblings. The total number of individual embryos used was 10, which was the same as the other conditions. The only difference is that in this condition, both retinas were collected from the same embryo, as opposed to only one retina being collected in the other conditions. Nonetheless, the genetic variability was maintained because the same number of individual embryos was used.
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 Young mutant retina, 36hpf, pool of twenty tissues, biological replicate 2
Data processing The probe-level data were background adjusted, normalized and summarized by a dChip (http://www.dchip.org) algorithm using default parameters.
 
Submission date Aug 24, 2007
Last update date Aug 14, 2011
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)
GSE8874 Factorial Microarray Analysis of Zebrafish Retinal Development

Data table header descriptions
ID_REF
VALUE The probe-level data were background adjusted, normalized and summarized by a dChip (http://www.dchip.org) algorithm using default parameters.

Data table
ID_REF VALUE
AFFX-BioB-3_at 155.8
AFFX-BioB-5_at 230.738
AFFX-BioB-M_at 209.688
AFFX-BioC-3_at 598.52
AFFX-BioC-5_at 559.152
AFFX-BioDn-3_at 1713.41
AFFX-BioDn-5_at 896.771
AFFX-CreX-3_at 7558.87
AFFX-CreX-5_at 4995.31
AFFX-DapX-3_at 429.361
AFFX-DapX-5_at 104.955
AFFX-DapX-M_at 174.583
AFFX-Dr-AB076373-1_at 39.7078
AFFX-Dr-acta1-3_at 0
AFFX-Dr-acta1-5_at 65.0823
AFFX-Dr-acta1-5_x_at 213.115
AFFX-Dr-acta1-M_at 167.951
AFFX-Dr-AF292559-1_at 18.4226
AFFX-Dr-AF292559-2_s_at 36.0835
AFFX-Dr-AF292559-3_s_at 0

Total number of rows: 15617

Table truncated, full table size 374 Kbytes.




Supplementary file Size Download File type/resource
GSM224828.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM224828.EXP.gz 518 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table

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