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Sample GSM257407 Query DataSets for GSM257407
Status Public on Feb 29, 2008
Title Unamputated adult caudal fin 2
Sample type RNA
Source name Adult male AB Zebrafish unamputated caudal fin, Replicate 2
Organism Danio rerio
Characteristics Adult male AB Zebrafish unamputated caudal fin.
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. For unamputated control, RNA was isolated from the non regenerating caudal fin. 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 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 The caudal fin of adult zebrafish were amputated. Unamputated fin tissue as well as regenerating fin tissue was collected at 1, 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 16, 2008
Last update date Feb 28, 2008
Contact name Robert L Tanguay
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

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

Data table
AFFX-BioB-3_at 1.518165231
AFFX-BioB-5_at 1.938118935
AFFX-BioB-M_at 2.103271723
AFFX-BioC-3_at 1.590827465
AFFX-BioC-5_at 1.710018516
AFFX-BioDn-3_at 1.373221755
AFFX-BioDn-5_at 1.491482139
AFFX-CreX-3_at 1.096390009
AFFX-CreX-5_at 1.233081818
AFFX-DapX-3_at 7.221007824
AFFX-DapX-5_at 1.25828743
AFFX-DapX-M_at 4.13160944
AFFX-Dr-AB076373-1_at 0.500422597
AFFX-Dr-acta1-3_at 0.584165752
AFFX-Dr-acta1-5_at 0.536508739
AFFX-Dr-acta1-5_x_at 1
AFFX-Dr-acta1-M_at 1.061699986
AFFX-Dr-AF292559-1_at 0.402934641
AFFX-Dr-AF292559-2_s_at 1.597442746
AFFX-Dr-AF292559-3_s_at 1.066028476

Total number of rows: 15617

Table truncated, full table size 434 Kbytes.

Supplementary file Size Download File type/resource
GSM257407.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM257407.CHP.gz 89.1 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file

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