|
| Status |
Public on Jun 30, 2020 |
| Title |
Control juvenile (Cy5) vs trf mutant (Cy3) 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control juvenile
|
| Organism |
Ciona intestinalis |
| Characteristics |
phenotype: Normal
morphology: juvenile
|
| Treatment protocol |
To obtain a progeny group including homozygous trf mutant larvae, trf heterozygous mutant at the reproductive stage was subjected to self-fertilization. At 42 hours post fertilization, approximately 50 swimming larvae which showed trf/trf phenotype were collected. As controls with normal phenotype, swimming larvae which have not started metamorphosis yet and juvenile which have completed tail regression were obtained from the same batch of trf mutant.
|
| Growth protocol |
trf is a mutant line of Ciona intestinalis isolated from a wild population. trf heterozygous mutants were kept under constant light to induce oocyte maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample by the acid guanidium thiocyanate-phenol-chloroform method.
|
| Label |
Cy5
|
| Label protocol |
Cyanine-5 (Cy5) or cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng of 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.
|
| |
|
| Channel 2 |
| Source name |
trf/trf mutant larva
|
| Organism |
Ciona intestinalis |
| Characteristics |
phenotype: trf/trf mutant
morphology: swimming larva initiating body axis rotation without tail regression
|
| Treatment protocol |
To obtain a progeny group including homozygous trf mutant larvae, trf heterozygous mutant at the reproductive stage was subjected to self-fertilization. At 42 hours post fertilization, approximately 50 swimming larvae which showed trf/trf phenotype were collected. As controls with normal phenotype, swimming larvae which have not started metamorphosis yet and juvenile which have completed tail regression were obtained from the same batch of trf mutant.
|
| Growth protocol |
trf is a mutant line of Ciona intestinalis isolated from a wild population. trf heterozygous mutants were kept under constant light to induce oocyte maturation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from each sample by the acid guanidium thiocyanate-phenol-chloroform method.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-5 (Cy5) or cyanine-3 (Cy3) labeled cRNAs were synthesized from 200 ng of 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 (750ng 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 |
Dye swap of M5Cj3-2. Biological replicate 2 of 2.
|
| 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 |
Jan 04, 2019 |
| Last update date |
Jul 01, 2020 |
| 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) |
| GSE124672 |
Identification of differentially expressed genes in the mutant tail regression failed (trf) in Ciona intestinalis. |
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