|
| Status |
Public on Aug 01, 2015 |
| Title |
Degenerating-3d-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
regenerating siphon 3 days
|
| Organism |
Ciona intestinalis |
| Characteristics |
treatment: regenerating siphon
days: 3 days
|
| Treatment protocol |
Regenerating oral siphons were compared to control siphons. For regenerating oral siphons, the entire siphon was removed from animals, and allowed to regenerate for 3, 6, or 9 days. After regeneration was complete, the regenerated siphons were removed from the animals and used for RNA extraction. For control animals, the entire oral siphon was removed and used for RNA.
|
| Growth protocol |
Animals were obtained by collection from marine environments nearly Woods Hole, MA., USA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from five or six siphones and purified using RNAeasy micro kit (QIAGEN) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng total RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
A set of fluorescently labeled cRNA targets (1.5ug for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.
|
| Scan protocol |
Hybridized microarrays were scanned on an Agilent Technologies G2565BA Microarray Scanner System.
|
| Description |
Gene expression in regeneration siphons 3 days after excision
3d-1
|
| Data processing |
The intensity of probes was extracted from scanned microarray images using Feature Extraction 10.5 software (Agilent Technologies). All algorithms and parameters used in this analysis were the default condition of the software. Some probes which were judged beyond analysis by Feature Extraction 10.5 software were eliminated from the following analysis.
|
| |
|
| Submission date |
Jul 10, 2014 |
| Last update date |
Aug 01, 2015 |
| Contact name |
Mayuko Hamada |
| E-mail(s) |
hamadam@okayama-u.ac.jp
|
| Organization name |
Okayama University
|
| Lab |
Ushimado Marine Institute
|
| Street address |
130-17, Kashino, Ushimado
|
| City |
Setouchi |
| State/province |
Okayama |
| ZIP/Postal code |
701-4303 |
| Country |
Japan |
| |
|
| Platform ID |
GPL5576 |
| Series (1) |
| GSE59280 |
Microarray Analysis Reveals a Role of the Notch System in Ciona Siphon Regeneration |
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