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Sample GSM257258 Query DataSets for GSM257258
Status Public on Feb 29, 2008
Title 2dpa tcdd 3
Sample type RNA
 
Source name 2 day post amputation fin; TCDD Exposed; replicate 3
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 0.5ng/mL TCDD (>99% pure, Chemsyn, Lenexa, KS) in the water for 1 hr. After several rinses in TCDD free water, the larvae were reared until 2 and 3 days post amputation (dpa) when their 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 (+/-TCDD) at 2 and 3 dpa 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 TCDD or vehicle. Regenerating fin tissue was collected at 2 and 3 days 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 Jan 15, 2008
Last update date Feb 28, 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)
GSE10184 2 or 3 Day Post Amputation Vehicle or TCDD Exposed

Data table header descriptions
ID_REF
VALUE signal intensity after GC-RMA preprocessing and each gene is normalized to the median

Data table
ID_REF VALUE
AFFX-BioB-3_at 0.861826599
AFFX-BioB-5_at 1.035443664
AFFX-BioB-M_at 0.974345326
AFFX-BioC-3_at 0.939308345
AFFX-BioC-5_at 1.013941288
AFFX-BioDn-3_at 0.859236538
AFFX-BioDn-5_at 0.806661665
AFFX-CreX-3_at 0.871043801
AFFX-CreX-5_at 0.836871028
AFFX-DapX-3_at 0.781846166
AFFX-DapX-5_at 0.709387958
AFFX-DapX-M_at 0.519779325
AFFX-Dr-AB076373-1_at 0.425545931
AFFX-Dr-acta1-3_at 0.571189523
AFFX-Dr-acta1-5_at 0.250701308
AFFX-Dr-acta1-5_x_at 2.20853591
AFFX-Dr-acta1-M_at 1.493158817
AFFX-Dr-AF292559-1_at 0.386436909
AFFX-Dr-AF292559-2_s_at 0.830149353
AFFX-Dr-AF292559-3_s_at 0.734114885

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM257258.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM257258.CHP.gz 89.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file
Processed data provided as supplementary file

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