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Sample GSM257405 Query DataSets for GSM257405
Status Public on Feb 29, 2008
Title 1dpa con 3
Sample type RNA
 
Source name 1 day post amputation larval regenerating fin; 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. The caudal fin at 2dpf were used as the unamputaed control and the larvae were reared until 1, 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, 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 at 2dpf, and 1, 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 was amputated. Regenerating fin tissue was collected at 2dpf, 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
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

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
AFFX-BioB-5_at 1.002344489
AFFX-BioB-M_at 0.9665007
AFFX-BioC-3_at 0.99999994
AFFX-BioC-5_at 1
AFFX-BioDn-3_at 1.068886042
AFFX-BioDn-5_at 1.006838322
AFFX-CreX-3_at 1.122800112
AFFX-CreX-5_at 1.045994043
AFFX-DapX-3_at 0.431485325
AFFX-DapX-5_at 0.723033905
AFFX-DapX-M_at 1.009595633
AFFX-Dr-AB076373-1_at 0.435550123
AFFX-Dr-acta1-3_at 189.0448608
AFFX-Dr-acta1-5_at 0.391881406
AFFX-Dr-acta1-5_x_at 0.913228333
AFFX-Dr-acta1-M_at 78.48747253
AFFX-Dr-AF292559-1_at 0.368415058
AFFX-Dr-AF292559-2_s_at 1.023805976
AFFX-Dr-AF292559-3_s_at 0.91675961

Total number of rows: 15617

Table truncated, full table size 431 Kbytes.




Supplementary file Size Download File type/resource
GSM257405.CEL.gz 2.2 Mb (ftp)(http) CEL
GSM257405.CHP.gz 88.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Raw data provided as supplementary file

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