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Sample GSM272738 Query DataSets for GSM272738
Status Public on Jan 31, 2009
Title 1dpa control 2
Sample type RNA
Source name 1 day post amputation larval regenerating fin; replicate 2
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
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

Data table
AFFX-BioB-3_at 0.969921172
AFFX-BioB-5_at 0.898863673
AFFX-BioB-M_at 0.941747069
AFFX-BioC-3_at 0.93645227
AFFX-BioC-5_at 0.92955333
AFFX-BioDn-3_at 0.917379379
AFFX-BioDn-5_at 0.99337405
AFFX-CreX-3_at 0.997529864
AFFX-CreX-5_at 0.958724558
AFFX-DapX-3_at 1.039651632
AFFX-DapX-5_at 0.58356595
AFFX-DapX-M_at 1.010327816
AFFX-Dr-AB076373-1_at 0.369903594
AFFX-Dr-acta1-3_at 1.043959856
AFFX-Dr-acta1-5_at 0.204316065
AFFX-Dr-acta1-5_x_at 1.083454132
AFFX-Dr-acta1-M_at 1.058350086
AFFX-Dr-AF292559-1_at 0.332008153
AFFX-Dr-AF292559-2_s_at 0.897840977
AFFX-Dr-AF292559-3_s_at 0.807507634

Total number of rows: 15617

Table truncated, full table size 436 Kbytes.

Supplementary file Size Download File type/resource
GSM272738.CEL.gz 2.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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