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Sample GSM1386057 Query DataSets for GSM1386057
Status Public on May 14, 2014
Title 16wkHFD_v_207
Sample type RNA
 
Source name 16wkHFD_visceral adipose
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: LDLR-/-
gender: male
age: 10-14 wks at the start of the experiment
treatment group: HFD for 16wks
tissue: Visceral adipose tissue
total duration: 16 weeks
Treatment protocol During a run-in period of nine weeks, mice were fed Western type, lard based high fat diet (HFD; Research Diets, New Brunswick, NJ; Diet D12541) to establish experimental conditions of obesity-associated hyperglycemia, hyperinsulinemia, hypertriglyceridemia and hypercholesterolemia. One group (n=9) remained on maintenance chow throughout the entire study period (16 weeks) and served as healthy, age-matched control. After the nine week run-in period, the HFD fed mice were matched into thirteen groups based on body weight. The first group (n=9) was sacrificed immediately after matching. The second group (n=15) was continued on HFD until the end of the experiment at t=16 weeks. The fourth group (n=9) was switched to regular chow (dietary lifestyle intervention). The other groups (each n=9) continued on HFD supplemented with drugs typically used in clinical practice. More specifically, following drugs were mixed into HFD ; rosiglitazone (0.010% w/w), pioglitazone (0.010% w/w), T0901317 (0.010% w/w) and salicylate (0.40% w/w).
Growth protocol Male LDLr-/- mice, age 10-14 weeks at the start of the experiment, originated from JAX (The Jackson Laboratory, Bar Harbor, Maine 04609, USA) and (3 mice per cage) with a 12 h light-dark cycle (7 a.m.-7 p.m. lights on). The mice had free access to food and water and remained on maintenance chow (Sniff R/M diet V1530, Uden, The Netherlands) until the start of the study. The mice had free access to food and water and remained on maintenance chow (Sniff R/M diet V1530, Uden, The Netherlands) until the start of the study.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the NucleoSpin RNA II kit from Macherey-Nagel. RNA samples (eluted in water) were stored at -80 degrees C.
Label biotin
Label protocol The quality control of RNA samples, RNA labelling and hybridisation were performed at ServiceXS (Leiden, The Netherlands). RNA concentration and purity were assessed using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, U.S.A). The RNA quality and integrity was determined using Lab-on-Chip analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, U.S.A.). Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturers specifications starting with 500 ng total RNA.
 
Hybridization protocol Per sample, 750ng of cRNA was used to hybridise to the MouseRef-8 v2 Expression BeadChip (Illumina, Inc., San Diego, CA, U.S.A.). Hybridisation and washing were performed according to the Illumina standard assay procedure.
Scan protocol Scanning was performed on the Illumina BeadStation 500 (Illumina, Inc., San Diego, CA, U.S.A.).
Data processing Image analysis and extraction of raw and background subtracted expression data were performed with Illumina Genomestudio Gene Expression software using default settings. The probe-level, background subtracted expression values were used as input for lumi package (Du et al. 2008) of the R/Bioconductor project (http://www.bioconductor.org; http://www.r-project.org). Probes were reannotated from the lumi generated nuID identifiers to illumina probeset identifiers using the lumiMouseAll.db bioconductor annotation package (bioconductor version 2.09). The lumi package was used to perform quality control of raw and normalised data and a quantile normalisation. After the normalisation, unexpressed probes were removed from the further analyses. To be considered expressed, signal detection p-value of the probe was required to be lower than 0.01 in at least one of experiments.
 
Submission date May 14, 2014
Last update date May 14, 2014
Contact name Thomas Kelder
Organization name TNO
Department Microbiology & Systems Bioloby
Street address Utrechtseweg 48
City Zeist
ZIP/Postal code 3704HE
Country Netherlands
 
Platform ID GPL6885
Series (1)
GSE57659 Transcription profiling by array of adipose samples from LDLR-/- mice to study response to anti-diabetic drug and dietary lifestyle interventions

Data table header descriptions
ID_REF
VALUE log2 quantile normalized

Data table
ID_REF VALUE
ILMN_2896528 12.47006098
ILMN_2721178 10.85106168
ILMN_3033922 11.47766688
ILMN_3092673 13.17269176
ILMN_2816356 5.744715682
ILMN_2808939 8.695023609
ILMN_2634564 8.304856368
ILMN_2737647 5.259526305
ILMN_2734484 8.855564441
ILMN_2952292 6.652244352
ILMN_2699078 5.477333332
ILMN_1213681 8.430344682
ILMN_2735413 5.540371237
ILMN_2735415 5.534966384
ILMN_2891688 9.122961481
ILMN_2637698 10.43174236
ILMN_2674228 8.654391897
ILMN_2601546 5.513028026
ILMN_2848071 4.773999937
ILMN_1248518 5.730839893

Total number of rows: 19513

Table truncated, full table size 474 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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