|
| Status |
Public on Feb 27, 2019 |
| Title |
WT zebrafish kept in darkness |
| Sample type |
RNA |
| |
|
| Source name |
WT Dark
|
| Organism |
Danio rerio |
| Characteristics |
treatment: dark
genotype: wild type
tissue: Whole body of larva
developmental stage: 6 day post fertilization
|
| Treatment protocol |
WT, zPer2 zCry1a double KO (DKO) , and zPer2 zCry1a zCry2a triple KO (TKO) zebrafish were kept in constant darkness after fertilization. They were then treated with light for 3- or 12-h at 6 dpf, or kept in constant darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from zebrafish treated as described in figure legends using Trizol Reagent (Invitrogen). The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and further by absorption spectrophotometry.
|
| Label |
Cy3
|
| Label protocol |
cDNAs were synthesized by the Low Input Quick Amp Labeling Kit. Cy3-labelled cRNA was synthesized by in vitro transcription with T7 RNA Polymerase.
|
| |
|
| Hybridization protocol |
RNA quality assurance, cDNA synthesis, and cRNA labeling and hybridization were carried out by Takara Bio Inc. (Otsu, Japan) using a Zebrafish (V3) Gene Expression Microarray 4X44K, the Low Input Quick Amp Labeling Kit, the Gene Expression Hybridization Kit, and the Gene Expression Wash Buffers Pack (all from Agilent Technologies) according to the manufacturer’s protocols.
|
| Scan protocol |
Genechips scanned using an Agilent DNA Microarray Scanner (G2565CA)
|
| Description |
Gene expression in WT zebrafish kept in darkness
|
| Data processing |
Microarray data were processed using GeneChip Operating Software (Feature Extraction)
|
| |
|
| Submission date |
Mar 07, 2018 |
| Last update date |
Feb 27, 2019 |
| Contact name |
Jun Hirayama |
| E-mail(s) |
hirayama.dbio@mri.tmd.ac.jp
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Medical Research Institute
|
| Lab |
Department of Developmental and Regenerative Biology
|
| Street address |
1-5-45 Yushima, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14688 |
| Series (1) |
| GSE111521 |
Light-dependent expression profiles in WT, DKO, and TKO zebrafish |
|
