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Sample GSM269736 Query DataSets for GSM269736
Status Public on Feb 29, 2008
Title 1 dpa con e (adult and larval fin study)
Sample type RNA
 
Source name Adult Male Zebrafish Caudal Fin 1 Day Post Amputaion, Vehicle Exposed Replicate E
Organism Danio rerio
Characteristics Adult Male Zebrafish AB Strain Caudal Fin 1 Day Post Amputaion, Vehicle Exposed
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 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 GSM85189

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 0.322664678
AFFX-BioB-5_at 0.377627194
AFFX-BioB-M_at 0.48359701
AFFX-BioC-3_at 0.365044415
AFFX-BioC-5_at 0.374819249
AFFX-BioDn-3_at 0.637244105
AFFX-BioDn-5_at 0.636284649
AFFX-CreX-3_at 0.693135083
AFFX-CreX-5_at 0.617899179
AFFX-DapX-3_at 5.772114277
AFFX-DapX-5_at 12.55528069
AFFX-DapX-M_at 16.90580368
AFFX-Dr-AB076373-1_at 0.616189957
AFFX-Dr-acta1-3_at 0.642315865
AFFX-Dr-acta1-5_at 0.377684087
AFFX-Dr-acta1-5_x_at 1.655571222
AFFX-Dr-acta1-M_at 1.025991082
AFFX-Dr-AF292559-1_at 0.325538248
AFFX-Dr-AF292559-2_s_at 0.603699386
AFFX-Dr-AF292559-3_s_at 0.661819696

Total number of rows: 15617

Table truncated, full table size 434 Kbytes.




Supplementary file Size Download File type/resource
GSM269736.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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