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Sample GSM1580820 Query DataSets for GSM1580820
Status Public on Jan 08, 2018
Title Vitd.10nM_2, biological replicate #2
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 9.063
A_55_P1991598 6.861
A_55_P2022211 9.043
A_55_P1980764 7.441
A_55_P1964375 12.981
A_51_P128876 14.503
A_51_P207591 17.485
A_55_P2131920 11.847
A_55_P2404223 10.692
A_55_P2101944 16.062
A_52_P358860 12.262
A_51_P119031 12.087
A_51_P343900 13.666
A_51_P234359 8.42
A_51_P487813 14.065
A_52_P613977 13.403
A_55_P1957209 7.556
A_52_P549166 8.821
A_55_P2052210 15.986
A_51_P128987 16.106

Total number of rows: 30094

Table truncated, full table size 586 Kbytes.

Supplementary file Size Download File type/resource
GSM1580820_Souris_6.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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