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| Status |
Public on Feb 25, 2010 |
| Title |
Zebrafish regenerating heart after 3 days post-amputation - replicate 2 (3DPA2) |
| Sample type |
RNA |
| |
|
| Source name |
Zebrafish regenerating heart after 3 days post-amputation
|
| Organism |
Danio rerio |
| Characteristics |
protocol: amputated
tissue: heart
time: 3 day post-amputation
|
| Treatment protocol |
Wild-type AB line zebrafish were maintained at 28.5ºC by standard methods (Raya et al. 2003) in the animal facilities of the Salk Institute for Biological Studies (La Jolla, San Diego, USA) and the Biomedical Research Park in Barcelona (Spain).
Sham-operated and regenerating hearts at 1, 3, 5 and 7 days post-amputation (dpa) were harvested by pulling from the outflow tract and the sinus venosus and put into PBS. Once in PBS, the outflow tract and the atrium were removed and the ventricles were washed from blood by letting it flow into the buffer and gently pressing the tissue.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen) after disrupting the tissue with RNAse-free pistons (BioBlock) and further homogenization by passing the suspension through a 25G needle and a 1ml syringe. An additional clean-up protocol including DNAse I digestion was performed using RNeasy Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturers protocols (Affymetrix, Santa Clara, CA) as descrived previously (Virtaneva et al., 2001).
1 to 2 µg of total RNA was used for biotin-cRNA labeling, fragmentation and hybridization onto the Affymetrix GeneChip® Zebrafish Genome Array (Affymetrix).
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| |
|
| Hybridization protocol |
1 to 2 µg of total RNA was used for biotin-cRNA labeling, fragmentation and hybridization onto the Affymetrix GeneChip® Zebrafish Genome Array (Affymetrix).
|
| Scan protocol |
Default settings for the Affymetrix GeneChip Scanner (7G upgrade)
|
| Description |
Heart samples from heart-amputated zebrafish 3 days post amputation.
|
| Data processing |
Data were processed using the affy and gcrma packages of Bioconductor (Gentleman et al. 2004) in R. Briefly, data were imported in R, and normalized using the gcrma normalization. As data were obtained in 3 batches, a batch correction procedure (Johnson, W. E., C. Li, et al. 2007) was applied in order to homogenize the data.
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| |
|
| Submission date |
Sep 07, 2009 |
| Last update date |
Mar 29, 2010 |
| Contact name |
Stephanie Boue |
| Organization name |
CMRB
|
| Street address |
Dr Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
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