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Sample GSM271863 Query DataSets for GSM271863
Status Public on Jan 31, 2009
Title 1dpa Beclo 2
Sample type RNA
 
Source name 1 day post amputation fin; Beclo Exposed; replicate 2
Organism Danio rerio
Characteristics AB strain larval zebrafish - regenerating caudal fin
Extracted molecule total RNA
Extraction protocol Caudal fins from two day old embryos (AB strain, Eugene, OR) were amputated and the animals were exposed to either DMSO (vehicle control) or 1uM Beclomethasone (Sigma) in the water for 1dpa. After several rinses in fish water, the regenerating fin tissue was amputated and collected for RNA analysis. RNA was extracted from the fin tissue using the RNAqueous Micro kit (Ambion, Austin, TX). Three groups at each time point and treatment, each comprised of 150 larval fins, were pooled to make an individual replicate. The quality and quantity of RNA was analyzed by UV absorbance. The abundance of ribosomal RNA and degree of degradation was determined in electropherogram patterns using the 2100 Bioanalyzer and RNA 6000 Nano chips (Agilent Technologies, Palo Alto, CA).
Label Labeling and probe processing was conducted under manufactures recommendations.
Label protocol A total of 100ng of RNA from the larval fin tissue (+/-Beclomethsone) at 1dpa were used to generate biotinylated complementary RNA (cRNA) using the Two-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA).
 
Hybridization protocol Hybridization was conducted as stipulated by Affymetrix GeneChip Expression Analysis Technical Manual (701021 Rev. 5).
Scan protocol Affymetrix fluidics station 400 was used to wash the arrays. Arrays were scanned with an Affymetrix scanner 3000.
Description The caudal fin of zebrafish larvae at 2day post fertilization were amputated, follwed by exposure with Beclomethsone or vehicle. Regenerating fin tissue was collected at 1days post amputation for mRNA abundance analysis.
Data processing Data was GC-RMA preprocessed and each gene was normalized to the median using Gene Spring 7.1 software.
 
Submission date Mar 07, 2008
Last update date Jul 21, 2008
Contact name Robert L Tanguay
E-mail(s) robert.tanguay@oregonstate.edu
Phone 541-737-6514
Organization name Oregon State University
Department EMT
Street address 1007 ALS
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
 
Platform ID GPL1319
Series (1)
GSE10766 1Day Post Amputation Vehicle or Beclomethasone Exposed

Data table header descriptions
ID_REF
VALUE GC-RMA

Data table
ID_REF VALUE
AFFX-BioB-3_at 0.940459549
AFFX-BioB-5_at 0.884057164
AFFX-BioB-M_at 0.875127912
AFFX-BioC-3_at 0.923300803
AFFX-BioC-5_at 0.979838789
AFFX-BioDn-3_at 0.941228449
AFFX-BioDn-5_at 0.932054937
AFFX-CreX-3_at 0.959306002
AFFX-CreX-5_at 0.862709403
AFFX-DapX-3_at 0.833169997
AFFX-DapX-5_at 0.643826067
AFFX-DapX-M_at 1.000727177
AFFX-Dr-AB076373-1_at 0.392022461
AFFX-Dr-acta1-3_at 0.956040144
AFFX-Dr-acta1-5_at 0.212629035
AFFX-Dr-acta1-5_x_at 1.098818779
AFFX-Dr-acta1-M_at 0.941650033
AFFX-Dr-AF292559-1_at 0.354289889
AFFX-Dr-AF292559-2_s_at 1.166542292
AFFX-Dr-AF292559-3_s_at 0.92549938

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM271863.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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