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Sample GSM257253 Query DataSets for GSM257253
Status Public on Feb 29, 2008
Title 3dpa con 1
Sample type RNA
 
Source name 3 day post amputation fin; Vehicle Exposed; replicate 1
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
Relations
Reanalyzed by GSM269746

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 1.198619485
AFFX-BioB-5_at 1.477164984
AFFX-BioB-M_at 1.349956274
AFFX-BioC-3_at 1.146030903
AFFX-BioC-5_at 1.316390276
AFFX-BioDn-3_at 1.165370941
AFFX-BioDn-5_at 1.246692181
AFFX-CreX-3_at 0.930087209
AFFX-CreX-5_at 1.068118811
AFFX-DapX-3_at 1.184075117
AFFX-DapX-5_at 0.718788505
AFFX-DapX-M_at 0.566577971
AFFX-Dr-AB076373-1_at 0.49834916
AFFX-Dr-acta1-3_at 0.991645515
AFFX-Dr-acta1-5_at 0.255097091
AFFX-Dr-acta1-5_x_at 0.994745851
AFFX-Dr-acta1-M_at 1.019917488
AFFX-Dr-AF292559-1_at 0.389592141
AFFX-Dr-AF292559-2_s_at 0.980442107
AFFX-Dr-AF292559-3_s_at 1.068769813

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM257253.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM257253.CHP.gz 88.5 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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