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Sample GSM971314 Query DataSets for GSM971314
Status Public on Aug 07, 2012
Title epid_KO_LF_1
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
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)
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
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
10338001 4170.048576
10338002 31.63364593
10338003 1267.460929
10338004 913.9151966
10338005 6.847071649
10338006 7.559899577
10338007 8.179986339
10338008 9.664153565
10338009 291.2955398
10338010 6.960862306
10338011 19.07978203
10338012 7.035285799
10338013 6.386671879
10338014 6.643071542
10338015 6.431492129
10338016 96.28950632
10338017 8360.517246
10338018 45.46392839
10338019 13.91245632
10338020 174.6350263

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM971314_G021_H10_06_epid_KO_LF.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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