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| Status |
Public on Oct 27, 2009 |
| Title |
Transcriptome analysis of the zebrafish pineal gland |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
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| Summary |
The zebrafish pineal gland (epiphysis) is an autonomous clock organ. In addition to being a site of melatonin production, it contains photoreceptor cells and functions as a circadian clock pace maker, making zebrafish a useful model system to study the developmental control of expression of genes associated with melatonin synthesis and photodetection, and the circadian clock. Here we have used DNA microarray technology to study the zebrafish pineal transcriptome. Analysis of gene expression at five different developmental stages (three embryonic and two adult) has revealed a highly dynamic transcriptional profile, revealing many genes that are highly expressed in the pineal gland. Statistical analysis of the data based on Gene Ontology (GO) annotation indicates that many transcription factors and cell cycle genes are highly expressed during embryonic stages, whereas genes dedicated to visual system signal transduction are preferentially expressed in the adult. Furthermore, several genes were identified that exhibit day/night differences in expression. Our data provide a rich source of candidate genes for distinct functions at different stages of pineal gland development.
Keywords: time course
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| Overall design |
Adults and embryos were kept under a 14-hr-light/10-hr-dark cycle. Pineal glands were isolated manually, guided by GFP fluorescence, from embryonic (3d, 5d, and 10d) and adult (3 month and 1-2 yr) transgenic zebrafish in which expression of the GFP gene is driven by the pineal-specific aanat2 promoter. For comparison, brain tissue from which the pineal gland and eyes had been removed was also collected (referred to as “brain”). Altogether, we collected 20 types of samples: five time points (3d, 5d, 10d, 3 mo, and 1-2 yr), two organs (pineal gland and brain), and two sampling times (day and night). For each type of sample, tissue was obtained and processed three to five times. Total RNA was prepared from each sample using the RNeasy Lipid Tissue Mini Kit (Qiagen) and biotin-labeled cDNA was generated using the Ovation Biotin system kit (NeuGen). The Affymetrix GeneChip® Zebrafish Genome Array was hybridized and processed using the standard Affymetrix protocol.
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| Contributor(s) |
Toyama R, Dawid IB |
| Citation(s) |
19504458 |
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| Submission date |
Oct 27, 2008 |
| Last update date |
Jan 25, 2018 |
| Contact name |
Reiko Toyama |
| E-mail(s) |
toyamar@mail.nih.gov
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| Phone |
301-496-9689
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| Fax |
301-496-0243
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| Organization name |
NIH
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| Department |
NICHD
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| Lab |
Lab. of Molecular Genetics
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| Street address |
Bldg.6B, Room 420, 9000 Rockville Pike
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (1) |
| GPL1319 |
[Zebrafish] Affymetrix Zebrafish Genome Array |
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| Samples (69)
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| GSM337575 |
3d, brain, day, rep1 |
| GSM337576 |
3d, brain, day, rep2 |
| GSM337577 |
3d, brain, day, rep3 |
| GSM337578 |
3d, pineal, night, rep1 |
| GSM337579 |
3d, pineal, night, rep2 |
| GSM337580 |
3d, pineal, night, rep3 |
| GSM337581 |
3d, pineal, night, rep4 |
| GSM337582 |
3d, brain, night, rep1 |
| GSM337583 |
3d, brain, night, rep2 |
| GSM337584 |
3d, brain, night, rep3 |
| GSM337585 |
3d, brain, night, rep4 |
| GSM337586 |
5d, pineal, day, rep1 |
| GSM337587 |
5d, pineal, day, rep2 |
| GSM337588 |
5d, pineal, day, rep3 |
| GSM337589 |
5d, pineal, day, rep4 |
| GSM337590 |
5d, pineal, day, rep5 |
| GSM337591 |
5d, brain, day, rep1 |
| GSM337592 |
5d, brain, day, rep2 |
| GSM337593 |
5d, brain, day, rep3 |
| GSM337594 |
5d, pineal, night, rep1 |
| GSM337595 |
5d, pineal, night, rep2 |
| GSM337596 |
5d, pineal, night, rep3 |
| GSM337597 |
5d, pineal, night, rep4 |
| GSM337598 |
5d, brain, night, rep1 |
| GSM337599 |
5d, brain, night, rep2 |
| GSM337600 |
10d, pineal, day, rep1 |
| GSM337601 |
10d, pineal, day, rep2 |
| GSM337602 |
10d, pineal, day, rep3 |
| GSM337603 |
10d, pineal, day, rep4 |
| GSM337604 |
10d, brain, day, rep1 |
| GSM337605 |
10d, brain, day, rep2 |
| GSM337606 |
10d, brain, day, rep3 |
| GSM337607 |
10d, pineal, night, rep1 |
| GSM337608 |
10d, pineal, night, rep2 |
| GSM337609 |
10d, pineal, night, rep3 |
| GSM337610 |
10d, pineal, night, rep4 |
| GSM337611 |
10d, brain, night, rep1 |
| GSM337612 |
10d, brain, night, rep2 |
| GSM337613 |
10d, brain, night, rep3 |
| GSM337614 |
10d, brain, night, rep4 |
| GSM337615 |
3mo, pineal, day, rep1 |
| GSM337616 |
3mo, pineal, day, rep2 |
| GSM337617 |
3mo, pineal, day, rep3 |
| GSM337618 |
3mo, brain, day, rep1 |
| GSM337619 |
3mo, brain, day, rep2 |
| GSM337620 |
3mo, brain, day, rep3 |
| GSM337621 |
3mo, pineal, night, rep1 |
| GSM337622 |
3mo, pineal, night, rep2 |
| GSM337623 |
3mo, pineal, night, rep3 |
| GSM337624 |
3mo, brain, night, rep1 |
| GSM337625 |
3mo, brain, night, rep2 |
| GSM337626 |
3mo, brain, night, rep3 |
| GSM337627 |
1yr, pineal, day, rep1 |
| GSM337628 |
1yr, pineal, day, rep2 |
| GSM337629 |
1yr, pineal, day, rep3 |
| GSM337630 |
1yr, pineal, day, rep4 |
| GSM337631 |
1yr, brain, day, rep1 |
| GSM337632 |
1yr, brain, day, rep2 |
| GSM337633 |
1yr, brain, day, rep3 |
| GSM337634 |
1yr, pineal, night, rep1 |
| GSM337635 |
1yr, pineal, night, rep2 |
| GSM337636 |
1yr, pineal, night, rep3 |
| GSM337637 |
1yr, pineal, night, rep4 |
| GSM337638 |
1yr, brain, night, rep1 |
| GSM337639 |
1yr, brain, night, rep2 |
| GSM337640 |
1yr, brain, night, rep3 |
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| Relations |
| BioProject |
PRJNA109795 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13371_RAW.tar |
125.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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