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Sample GSM879468 Query DataSets for GSM879468
Status Public on Apr 13, 2012
Title WAT_WT_HFD_αGalCer_repl2
Sample type RNA
Source name WAT_WT_HFD_αGalCer
Organism Mus musculus
Characteristics background strain: C57Bl/6J
genotype/variation: wild type
gender: male
age: 6.5 weeks
tissue: epididymal adipose tissue
Treatment protocol Six week-old mice were placed on a high fat diet (HFD) on day 0 with intraperitoneal injection of α-galactosylceramide (αGalCer; 100 ng/g bodyweight) or vehicle (pyridine) on day 0 and day 2. Mice were killed on day 4 by cervical dislocation and epididymal white adipose tissue was removed.
Growth protocol Wildtype C57/BL6 and B6.129S6-Cd1d1/Cd1d2tm1spb/J (CD1d-/-, #008881) were purchased from the Jackson Laboratory and bred in our facility.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from adipose tissue using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
Label biotin
Label protocol The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction. A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).
Hybridization protocol The Affymetrix GeneChip Mouse Gene 1.1 ST arrays are peg arrays arranged into the standard 96 well plate format. The 13 arrays that were used in this experiment were provided as subset of a 1x 16 array plate. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument.
Description epididymal adipose tissue, wild type mouse, after 4 days on a high fat diet, injected intraperitoneally with galactosylceramide (αGalCer) on days 0 and 2, replicate 2
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.18.1).
Submission date Feb 23, 2012
Last update date Apr 13, 2012
Contact name Guido Hooiveld
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
Platform ID GPL11533
Series (1)
GSE36032 Activation of natural killer T cells promotes M2 macrophage polarization in adipose tissue and improves systemic glucose tolerance via the IL-4/STAT6 signaling axis in obesity

Data table header descriptions
VALUE RMA signal (as log2)

Data table
10338001 10.44688143
10338002 4.801264424
10338003 8.980176547
10338004 8.170263889
10338005 2.17234343
10338006 2.52797261
10338007 2.813881171
10338008 3.181161437
10338009 6.951807113
10338010 2.231260353
10338011 4.28448529
10338012 2.380258028
10338013 2.000621874
10338014 2.127059208
10338015 2.010615066
10338016 5.764534278
10338017 11.4131219
10338018 5.135724088
10338019 3.919256684
10338020 6.668053456

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM879468_G023_E05_05_WT_HFD_AGALCER.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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