|
| Status |
Public on Nov 17, 2015 |
| Title |
control_VAT_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
visceral adipose tissue, control
|
| Organism |
Danio rerio |
| Characteristics |
line: MieKomachi 001
tissue: visceral adipose tissue
age: 4 mpf
phenotype: control
treatment: none
|
| Treatment protocol |
Zebrafish (MieKomachi 001 line created by crossing nacre and rose) in the OF and OF+RSV groups were fed three times per day with freshly hatched Artemia. Zebrafish in the OF+RSV group was fed with gluten containing RSV (corresponding to 20 μg /fish/day) at 20 min before feeding Artemia in morning. Zebrafish in the OF group were fed with gluten without RSV at 20 min before feeding Artemia in morning.
|
| Growth protocol |
Zebrafish were raised at 28.5 ± 0.5°C with a 14 h/10 h light/dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The adipose tissue was stored in RNA-later (Applied Biosystems, Foster City, CA, USA). Total RNA was then extracted using an RNeasy Plus Micro Kit (Qiagen, Valencia, CA, USA), qualified by an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and quantified using a spectrophotometer (NanoDrop ND-100, Wilmington, DE, USA).
|
| Label |
Cy3
|
| Label protocol |
Fifty nanograms of total RNA from each visceral AT depot were converted into labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent).
|
| |
|
| Hybridization protocol |
860 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing fragmentation buffer and blocking agent according to the manufacturer's protocol. After the fragmentation, 55 uL of hybridization buffer was added to the fragmentation mixture. For each reaction, 100 uL was hybridized to an Agilent-026437 Zebrafish DNA Oligo Microarray for 17 hours at 65°C in a rotating hybridization chamber. After the hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1, 1 minute with 37°C GE Wash buffer 2.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides.
|
| Description |
Gene expression in visceral adipose tissue from zebrafish.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 8.0 (Agilent). The data was normalized using limma package in Bioconductor. Features flagged in gIsSaturated, gIsFeatNonUnifOL, gIsPosAndSignif and gIsWellAboveBG were excluded from further analysis.
|
| |
|
| Submission date |
Jun 25, 2015 |
| Last update date |
Nov 17, 2015 |
| Contact name |
Yuhei Nishimura |
| E-mail(s) |
yuhei@med.mie-u.ac.jp
|
| Phone |
81-59-231-5411
|
| Organization name |
Mie University Graduate School of Medicine
|
| Department |
Integrative Pharmacology
|
| Street address |
2-174 Edobashi
|
| City |
Tsu |
| State/province |
Mie |
| ZIP/Postal code |
514-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL14664 |
| Series (1) |
| GSE70281 |
Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol in obesity |
|
