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Sample GSM1257988 Query DataSets for GSM1257988
Status Public on Nov 03, 2016
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
Submission date Nov 04, 2013
Last update date Nov 03, 2016
Contact name emmanuelle meugnier
Organization name INSERMU1060/INRA1397
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

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 12.5714860919481
2 4.48057313100772
3 4.4597362486311
4 3.75747089327862
5 3.19244347383915
6 4.06912633755765
7 4.07613682597839
8 4.70861354965021
9 4.53050732514972
10 4.39904221825972
11 4.30552092997906
12 6.92481830188229
13 5.32661024332479
14 11.1197427298673
15 6.31316910216576
16 11.2334135643047
17 14.8256584663556
18 5.32766092521572
19 5.38559550400998
20 15.4232099268363

Total number of rows: 44397

Table truncated, full table size 981 Kbytes.

Supplementary file Size Download File type/resource
GSM1257988_US45103047_252665511862_S01_GE1_107_Sep09_1_4.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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