NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM272739 Query DataSets for GSM272739
Status Public on Jan 31, 2009
Title 1dpa control 3
Sample type RNA
 
Source name 1 day post amputation larval regenerating fin; 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. 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 Mar 12, 2008
Last update date Jul 21, 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)
GSE10766 1Day Post Amputation Vehicle or Beclomethasone Exposed

Data table header descriptions
ID_REF
VALUE GC-RMA

Data table
ID_REF VALUE
AFFX-BioB-3_at 1.030078888
AFFX-BioB-5_at 0.9805547
AFFX-BioB-M_at 0.975748003
AFFX-BioC-3_at 1.019010186
AFFX-BioC-5_at 1.000370979
AFFX-BioDn-3_at 1.156411648
AFFX-BioDn-5_at 1.006626129
AFFX-CreX-3_at 1.061577439
AFFX-CreX-5_at 1.048128009
AFFX-DapX-3_at 0.700781167
AFFX-DapX-5_at 0.619817197
AFFX-DapX-M_at 1.009273887
AFFX-Dr-AB076373-1_at 0.395538539
AFFX-Dr-acta1-3_at 0.452410936
AFFX-Dr-acta1-5_at 0.21473439
AFFX-Dr-acta1-5_x_at 0.51974982
AFFX-Dr-acta1-M_at 0.343254983
AFFX-Dr-AF292559-1_at 0.354370952
AFFX-Dr-AF292559-2_s_at 1.018542528
AFFX-Dr-AF292559-3_s_at 0.889451504

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.




Supplementary file Size Download File type/resource
GSM272739.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap