|
| Status |
Public on Aug 31, 2016 |
| Title |
Bone-adult-female-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Bone
|
| Organism |
Oryzias latipes |
| Characteristics |
tissue: Bone
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogeneized and total RNAs were extracted using a Trizol® Reagent (Applied Biosystem, Foster city, CA, USA) following the manufacturer´s instructions. RNA integrity was checked with the Agilent Bioanalyzer (Agilent Technologies, Massy, France) and yield was estimated using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France).
|
| Label |
Cy3
|
| Label protocol |
MiRNA microarray was performed using miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent v2.2) according to the manufacturer procedure with slight modifications. Total RNA (200 ng) from each tissu with labeling Spike-In were dephosphorylated for 30 minutes at 37°C. RNA was denatured with DMSO at 100°C for 7 minutes. RNA was then labeled by terminal ligation of cyanine3-pCp using T4 ligase for 2 hours at 16°C. Purification of labeled RNA was done using Micro Bio-Spin column (Bio-Rad) to eliminate free cyanine3-pCp
|
| |
|
| Hybridization protocol |
Hybridization was performed at 55°C, 20 rpm for 20 hours. Slides were washed for 5 minutes with Wash 1 and 2 and immediately proceeded to scan.
|
| Scan protocol |
Agilent DNA Microarray Scanner (Agilent Technologies, Massy, France) and Scan Control software were used with the following protocol: profile: AgilentHD_miRNA, channels: Green, resolution: 3µm, TIFF: 20 bit.
|
| Description |
miRNAs expression
Bone-T10-F03
|
| Data processing |
Signal intensities were then quantified using FeatureExtraction software (Agilent). Spot with low signal (lower than three times the background level) were excluded. Data were processed by GeneSpring software (Agilent v.11.5.0) using GmedianSignal. Data were subsequently normalized using quantile normalization.
|
| |
|
| Submission date |
Apr 29, 2016 |
| Last update date |
Aug 31, 2016 |
| Contact name |
Julien Bobe |
| E-mail(s) |
Julien.Bobe@rennes.inra.fr
|
| Phone |
(33) 2 23 48 57 24
|
| Organization name |
Institut National de la Recherche Agronomique
|
| Lab |
INRA-SCRIBE
|
| Street address |
Campus de Beaulieu
|
| City |
Rennes |
| ZIP/Postal code |
35000 |
| Country |
France |
| |
|
| Platform ID |
GPL21776 |
| Series (1) |
| GSE80823 |
Identification of novel ovarian predominant miRNAs in medaka |
|
