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Sample GSM947572 Query DataSets for GSM947572
Status Public on Feb 27, 2013
Title High cholesterol diet HC + EZE rep5
Sample type RNA
 
Source name mouse liver
Organism Mus musculus
Characteristics strain: ApoE3Leiden
gender: female
treatment: High cholesterol diet HC+EZE
tissue: liver
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from individual livers (n=8 livers per group, 48 samples in total) using glass beads and RNAzol (Campro Scientific, Veenendaal, The Netherlands).
Label Biotin
Label protocol The Illumina® TotalPrep™ RNA Amplification Kit (Ambion, art. No. AM-IL1791) was used to synthesize biotin labeled cRNA starting with 500 ng total RNA. Concentration of the labeled cRNA was measured using the Nanodrop spectrophotometer.
 
Hybridization protocol We have used standard Illumina hybridisation protocol. The amount of biotinylated cRNA that was hybridized onto the MouseRef-8 Expression BeadChip was 750 ng
Scan protocol Illumina’s Genomestudio v1.1.1 software with the default settings advised by Illumina, was used for Gene Expression analysis. All the quality control data of this BeadChip were within specifications of the microarray service provider (Service XS, Leiden, the Netherlands).
Description 4991868003_G
Data processing Probe-level, background subtracted expression values were used as input for GeneSpring GX11 software (Agilent), which was used for normalization of data; threshold signals below the value of 5 were set at 5. To be considered expressed, the signal detection p-value of the probe had to be lower than 0.01 in at least 1 of 48 experiments. 15505 probes fulfilled these criteria. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
GeneSpring GX11 software (Agilent) was used to normalize data. Differential expression of probes was assessed using unpaired moderated t-test (LIMMA) via The Remote Analysis Computation for gene Expression data (RACE) suite at http://race.unil.ch
 
Submission date Jun 13, 2012
Last update date Feb 27, 2013
Contact name Lars Verschuren
E-mail(s) lars.verschuren@tno.nl
Phone +31888666039
Organization name TNO
Department Microbiology and Systems Biology
Street address Utrechtseweg 48
City Zeist
ZIP/Postal code 3704HE
Country Netherlands
 
Platform ID GPL6885
Series (1)
GSE38688 Systems biology analysis unravels complementary action of combined Rosuvastatin and Ezetimibe therapy

Data table header descriptions
ID_REF
VALUE quantile normalized minus non-expressed

Data table
ID_REF VALUE
ILMN_2607609 9.41
ILMN_3140158 6.20
ILMN_2674533 7.03
ILMN_1215893 5.57
ILMN_2910106 5.89
ILMN_2603725 9.93
ILMN_2899591 6.09
ILMN_2658355 12.22
ILMN_2836710 9.47
ILMN_2491859 5.99
ILMN_2764607 5.91
ILMN_2800655 11.18
ILMN_1247592 7.15
ILMN_2747196 9.70
ILMN_2942011 7.73
ILMN_3159156 6.74
ILMN_2675078 5.61
ILMN_2868579 9.48
ILMN_2625047 5.24
ILMN_2724530 5.61

Total number of rows: 15505

Table truncated, full table size 273 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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