|
| Status |
Public on Nov 03, 2016 |
| Title |
PALMITATE10 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 incubated with EXO-Palm
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C16
cell type: myoblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using Trizol (Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cyanine3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug 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 55µl containing 1x Agilent fragmentation buffer following the manufacturers instructions. On completion of the fragmentation reaction,55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100µl were hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed according to manufacturer's intructions
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides
|
| Description |
treated, biological replicate 1
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted . Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw data were normalized using bioconductor and limma package. Briefly, background substraction was performed using the normexp correction with an offset=1, then signals were normalized using quantile normalization. Only spots presenting a signal 10% brighter than the 95th percentile of the negative control are kept for statistical analysis
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| |
|
| Submission date |
Nov 04, 2013 |
| Last update date |
Nov 03, 2016 |
| Contact name |
emmanuelle meugnier |
| E-mail(s) |
emmanuelle.meugnier@univ-lyon1.fr
|
| Organization name |
INSERMU1060/INRAE1397
|
| Lab |
CarMeN
|
| Street address |
Cens Eli Bat 2 D- Hopital Lyon Sud
|
| City |
Pierre Bénite |
| ZIP/Postal code |
69495 |
| Country |
France |
| |
|
| Platform ID |
GPL10333 |
| Series (1) |
| GSE52048 |
Palmitate-induced inhibition of C2C12 insulin pathway modifies the release of exosomes and their biological actions on muscle cells |
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