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Sample GSM85197 Query DataSets for GSM85197
Status Public on Mar 20, 2006
Title 3 dpa tcdd b
Sample type RNA
 
Source name Adult Male Zebrafish Caudal Fin 3 Day Post Amputation, TCDD Exposed Replicate B
Organism Danio rerio
Characteristics strain: AB Zebrafish
age: Adult
gender: Male
time point: 3 day post amputation of caudal fin
exposure: TCDD
Treatment protocol Adult male zebrafish (Danio rerio) (AB strain, Eugene, OR) were anesthetized with tricaine methanesulfonate (MS-222) and their caudal fins were amputated at the bifurcation of the fin rays. Fish were then injected with phosphatidylcholine liposomes (vehicle control) alone or liposomes incorporated with TCDD (>99% pure, Chemsyn, Lenexa, KS) resulting in a final dose of 50 ng TCDD/g fish. At the indicated dpa, fish were euthanized with an over dose of MS-222. Regenerated fin tissue was then isolated by amputation within two ray segments anterior to the original amputation plane. Amputated tissue was then stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC until RNA was isolated from the tissue. Tissues from 10 fish were combined to comprise a single experimental group (replicate). Three groups of tissue were obtained from vehicle control or TCDD exposed fish at 1, 3, and 5 dpa.
Growth protocol Fish were matained at 27oC until under standard conditions.
Extracted molecule total RNA
Extraction protocol Amputated tissue was stored in RNAlater (Qiagen, Valencia, CA) and frozen at -80oC. RNAlater was removed from the samples and total RNA was purified with TRI reagent (Molecular Research Laboratories, Cincinnati, OH) according to the manufacturer’s instructions. Total RNA was DNase treated with RQ1 DNase (Promega, Madison, WI) according to the manufacture’s protocol and RNA quantity and quality was determined by UV absorbance. Ribosomal RNA abundance 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 2.5 µg of total RNA was used to generate biotinylated complementary RNA (cRNA) for each treatment group using the One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA). RNA was reverse transcribed using a T7-(dT)24 primer and Superscript II reverse transcriptase (Invitrogen, Carlsbad, 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 Adult male zebrafish were i.p. injected with 50 ng/g TCDD or vehicle and caudal fins were amputated. Regenerating fin tissue was collected at 1, 3 and 5 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 Nov 23, 2005
Last update date Jun 13, 2011
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)
GSE3667 1, 3, or 5 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-5_at 122.42177
AFFX-BioB-M_at 189.07877
AFFX-BioB-3_at 77.384636
AFFX-BioC-5_at 208.0408
AFFX-BioC-3_at 186.3974
AFFX-BioDn-5_at 1048.2985
AFFX-BioDn-3_at 1752.9506
AFFX-CreX-5_at 6234.3535
AFFX-CreX-3_at 11339.237
AFFX-DapX-5_at 180.12648
AFFX-DapX-M_at 461.48386
AFFX-DapX-3_at 680.81537
AFFX-LysX-5_at 22.175547
AFFX-LysX-M_at 28.18486
AFFX-LysX-3_at 90.96898
AFFX-PheX-5_at 35.484074
AFFX-PheX-M_at 44.732525
AFFX-PheX-3_at 101.12692
AFFX-ThrX-5_at 43.26081
AFFX-ThrX-M_at 34.02866

Total number of rows: 15617

Table truncated, full table size 402 Kbytes.




Supplementary file Size Download File type/resource
GSM85197.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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