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| Status |
Public on Oct 01, 2008 |
| Title |
Regenerating zebrafish fin fold vs. uncut control |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
|
| Summary |
Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration.
Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control.
Keywords: Stress response, injury response.
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| Overall design |
Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point.
For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturer’s instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 μg of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 μg, from ~130 tail tissues at 48 hpa or uncut control tissues.
Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.
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| Contributor(s) |
Kawakami A |
| Citation(s) |
18950614 |
| |
| Submission date |
May 08, 2008 |
| Last update date |
Mar 19, 2012 |
| Contact name |
Atsushi Kawakami |
| E-mail(s) |
atkawaka@bio.titech.ac.jp
|
| Phone |
+81-45-924-5717
|
| Fax |
+81-45-924-5718
|
| Organization name |
Tokyo Institute of Technology
|
| Department |
Biological Information
|
| Street address |
4259 Nagatsuta, Midori-ku
|
| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
| |
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| Platforms (2) |
| GPL530 |
MWG Zebrafish 14K-1 Array |
| GPL531 |
MWG Zebrafish 14K-2 Array |
|
| Samples (4)
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| GSM287608 |
18-24hpa regenerating fin fold vs. control |
| GSM287609 |
control vs. 48hpa regenerating fin fold |
| GSM287610 |
18-24hpa regenerating fin fold vs. control |
| GSM287611 |
control vs. 48hpa regenerating fin fold |
|
| Relations |
| BioProject |
PRJNA106513 |
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