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Sample GSM224829 Query DataSets for GSM224829
Status Public on Aug 04, 2008
Title YR_36hpf_rep3 (YR36_7-3)
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 3
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 163.913
AFFX-BioB-5_at 258.238
AFFX-BioB-M_at 236.911
AFFX-BioC-3_at 574.625
AFFX-BioC-5_at 571.271
AFFX-BioDn-3_at 1817.98
AFFX-BioDn-5_at 981.113
AFFX-CreX-3_at 5958.58
AFFX-CreX-5_at 4970.59
AFFX-DapX-3_at 405.469
AFFX-DapX-5_at 105.64
AFFX-DapX-M_at 244.846
AFFX-Dr-AB076373-1_at 45.8442
AFFX-Dr-acta1-3_at 0
AFFX-Dr-acta1-5_at 86.465
AFFX-Dr-acta1-5_x_at 603.908
AFFX-Dr-acta1-M_at 302.303
AFFX-Dr-AF292559-1_at 9.04736
AFFX-Dr-AF292559-2_s_at 34.4299
AFFX-Dr-AF292559-3_s_at 14.0071

Total number of rows: 15617

Table truncated, full table size 374 Kbytes.




Supplementary file Size Download File type/resource
GSM224829.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM224829.EXP.gz 521 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table

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