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Sample GSM269745 Query DataSets for GSM269745
Status Public on Feb 29, 2008
Title 2dpa con 3 (adult and larval fin study)
Sample type RNA
 
Source name 2 day post amputation fin; Vehicle 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 (Figure 1). 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 Feb 28, 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)
GSE10188 Comparative genomic analysis between adult and larval fin regeneration
Relations
Reanalysis of GSM257252

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 1.137285233
AFFX-BioB-5_at 1
AFFX-BioB-M_at 1.157417417
AFFX-BioC-3_at 1.089396238
AFFX-BioC-5_at 1.093951106
AFFX-BioDn-3_at 1.053780675
AFFX-BioDn-5_at 1.10296452
AFFX-CreX-3_at 0.941818893
AFFX-CreX-5_at 1.019093275
AFFX-DapX-3_at 0.300899148
AFFX-DapX-5_at 0.797979772
AFFX-DapX-M_at 0.665843129
AFFX-Dr-AB076373-1_at 0.422445208
AFFX-Dr-acta1-3_at 3.239484072
AFFX-Dr-acta1-5_at 0.389996618
AFFX-Dr-acta1-5_x_at 0.605366528
AFFX-Dr-acta1-M_at 0.865997672
AFFX-Dr-AF292559-1_at 0.356585473
AFFX-Dr-AF292559-2_s_at 1.15645206
AFFX-Dr-AF292559-3_s_at 0.818104208

Total number of rows: 15617

Table truncated, full table size 431 Kbytes.




Supplementary file Size Download File type/resource
GSM269745.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM269745.CHP.gz 88.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file

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