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Sample GSM1580817 Query DataSets for GSM1580817
Status Public on Jan 08, 2018
Title Vitd.10nM_1, biological replicate #1
Sample type RNA
Source name C2C12
Organism Mus musculus
Characteristics treatment: 10 nM 1,25 (OH)2-vitamine D3
Extracted molecule total RNA
Extraction protocol RNA was extracted with 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 Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp labeling One color : Cy3 (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 and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4*44K V2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides.
Description Gene expression after 72H of treatment with 10nM of Vitamin D
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters . Data treatment was performed with bioconductor and Limma library. Background substraction was performed using the Normexp correction with offset =50. Quantile normalization was then applied. Features flagged in Feature Extraction as control, as Feature Non-uniform outliers, saturating or too weak were excluded.
Submission date Jan 08, 2015
Last update date Jan 08, 2018
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 GPL11202
Series (1)
GSE64803 Impact of Vitamin D on murine myotubes

Data table header descriptions
VALUE Normalized Log2 signal intensity

Data table
A_55_P1989846 8.513
A_55_P1991598 6.982
A_55_P2022211 8.725
A_55_P1980764 8.506
A_55_P1964375 12.767
A_51_P128876 14.574
A_51_P207591 17.173
A_55_P2131920 11.636
A_55_P2404223 10.672
A_55_P2101944 15.956
A_52_P358860 12.112
A_51_P119031 11.739
A_51_P343900 13.303
A_51_P234359 8.708
A_51_P487813 13.633
A_52_P613977 13.236
A_55_P1957209 7.243
A_52_P549166 8.513
A_55_P2052210 15.778
A_51_P128987 16.022

Total number of rows: 30094

Table truncated, full table size 586 Kbytes.

Supplementary file Size Download File type/resource
GSM1580817_Souris_3.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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