|
| Status |
Public on Apr 13, 2012 |
| Title |
WAT_WT_HFD_vehicle_repl3 |
| Sample type |
RNA |
| |
|
| Source name |
WAT_WT_HFD_vehicle
|
| 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 vehicle on days 0 and 2, replicate 3
|
| 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 |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| 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 |
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