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Sample GSM971315 Query DataSets for GSM971315
Status Public on Aug 07, 2012
Title epid_KO_LF_2
Sample type RNA
Source name epididymal adipose tissue
Organism Mus musculus
Characteristics tissue: epididymal adipose tissue
strain: C57BL/6
genotype: CD1d-/-
diet: low fat
Treatment protocol Mice were age matched and fed standard chow until age 10-11 weeks, and subsequently fed LFD (10 kcal% fat, Research Diet D12450B) or HFD (45 kcal% fat, Research Diet D12451) for 18-19 weeks.
Growth protocol WT C57BL/6J mice (8 weeks; Charles River Laboratories) and CD1d-null mice that had been backcrossed to C57BL/6J for 10-12 generations were bred in our facility.
Extracted molecule total RNA
Extraction protocol Epididymal adipose tissue was excised and stored at −80C until analysis. RNA was extracted using Trizol (Invitrogen) and further purified on an RNeasy micro column (Qiagen). RNA samples from 4-6 mice per experimental group were pooled for microarray analysis.
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).
Hybridization protocol One hundred nanogram of RNA per sample was hybridized to an Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate (Santa Clara, CA) according to manufacturer's instructions.
Scan protocol Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.
Data processing Expression estimates were calculated using RMA using RMA using R version R-2.15.0 and Bioconductor 2.10
Submission date Jul 20, 2012
Last update date Aug 07, 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)
GSE39534 CD1d-restricted NKT cell function prevents insulin resistance in lean mice, and is regulated by adipocytes and is regulated by adipocytes

Data table header descriptions
VALUE log2 RMA signal

Data table
10338001 2655.775859
10338002 23.81812719
10338003 668.4163338
10338004 451.7111036
10338005 6.671245493
10338006 7.140193277
10338007 7.686520786
10338008 8.960694541
10338009 160.2493043
10338010 6.676470646
10338011 15.64187378
10338012 6.821656096
10338013 6.274587654
10338014 6.473843292
10338015 6.297175474
10338016 56.80876154
10338017 6190.105465
10338018 31.44107749
10338019 12.25057122
10338020 104.2696908

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.

Supplementary file Size Download File type/resource
GSM971315_G021_H12_08_epid_KO_LF.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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