|
| Status |
Public on Mar 16, 2017 |
| Title |
ExVivo liver_13 |
| Sample type |
RNA |
| |
|
| Source name |
Mice transplanted with lean microbiota
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: liver
gender: male
age: 10 weeks
|
| Treatment protocol |
Mice have been transplanted with the vehicle (reduced PBS), or lean or obese gut microbiota.
|
| Growth protocol |
6-wk-old C57Bl/6 male mice were fed a normal chow (NC) for 4 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
liver total RNAs has been prepared by the miRNeasy QIAGEN kit
|
| Label |
Cy3
|
| Label protocol |
For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked with the Nanodrop ND2000 spectrophotometer (Thermo Scientific).
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809 enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).
|
| Scan protocol |
Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software
|
| Description |
Mice transplanted with lean microbiota
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library.
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
Mar 16, 2017 |
| Contact name |
Matteo Serino |
| E-mail(s) |
matteo.serino@inserm.fr
|
| Organization name |
INSERM UMR1220-IRSD
|
| Street address |
Baylac place
|
| City |
Toulouse |
| ZIP/Postal code |
31024 |
| Country |
France |
| |
|
| Platform ID |
GPL21810 |
| Series (1) |
| GSE81318 |
Gut microbiota transplantation in conventional mice |
|
