|
| Status |
Public on Sep 24, 2011 |
| Title |
Zebrafish-embryo_100uM-DEM-treated_3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
DMSO-12h
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: wild type
developmental stage: embryo
|
| Biomaterial provider |
Tsukuba university
|
| Treatment protocol |
Embryo were treated with culture media containing 0.1% DMSO from 96 hour post fertilization (hpf) to 108 hpf.
|
| Growth protocol |
All embryos were incubated at 28℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The collected zebrafish embryos were quickly homogenized with 1ml of QIAzol reagent (Qiagen), and subsequently stored at -80°C. Total RNA was extracted according to the manufacturer’s instructions. Isolated total RNA was further purified using RNAeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Amino-allyl-modified amplified RNA (aRNA) was synthesized in one amplification round from 1 μg of purified total RNA using the amino-allyl RNA amplification kit (Sigma-Aldrich). Subsequently, 5 μg of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 and Cy5dyes (GE Healthcare) and column purified.
|
| |
|
| Channel 2 |
| Source name |
DEM-12h
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: wild type
developmental stage: embryo
|
| Biomaterial provider |
Tsukuba university
|
| Treatment protocol |
Embryo were treated with culture media containing 100 µM diethylmaleate (DEM) from 96 hour post fertilization (hpf) to 108 hpf.
|
| Growth protocol |
All embryos were incubated at 28℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The collected zebrafish embryos were quickly homogenized with 1ml of QIAzol reagent (Qiagen), and subsequently stored at -80°C. Total RNA was extracted according to the manufacturer’s instructions. Isolated total RNA was further purified using RNAeasy mini kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Amino-allyl-modified amplified RNA (aRNA) was synthesized in one amplification round from 1 μg of purified total RNA using the amino-allyl RNA amplification kit (Sigma-Aldrich). Subsequently, 5 μg of amino-allyl-modified aRNA was used for coupling of monoreactive Cy3 and Cy5dyes (GE Healthcare) and column purified.
|
| |
|
| |
| Hybridization protocol |
The dual-color hybridization of the MZH chips was performed according to the manufacture’s instructions of AceGene DNA microarray (Hitachi-soft). Each experiment was repeated in triplicate.
|
| Scan protocol |
After hybridization, MZH chips were scanned using Affimetrix 428 array scanner (Affimetrix).
|
| Data processing |
Microarray data were processed from raw data image files with Affymetrix Jaguar (Affimetrix) and normalized. Processed data were subsequently imported into Excel (Microsoft) to compare expression profiles of DEM treated samples to that of control samples.
|
| |
|
| Submission date |
Sep 21, 2011 |
| Last update date |
Sep 24, 2011 |
| Contact name |
Shin'ichi Akiyama |
| E-mail(s) |
akiyama@med.nagoya-u.ac.jp
|
| Organization name |
Nagoya University Graduate School of Medicine
|
| Department |
Department of Nephrology
|
| Street address |
65 Tsurumaicho
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14379 |
| Series (1) |
| GSE32267 |
Zebrafish embryo response to Diethyl maleate |
|
