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Sample GSM397559 Query DataSets for GSM397559
Status Public on Mar 31, 2010
Title SubcutaneousFat.HFD.4
Sample type RNA
 
Source name Subcutaneous Fat: HFD
Organism Mus musculus
Characteristics strain: DBA/2J
tissue: Subcutaneous Fat
treatment: high fat diet
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by TRIzolTM Plus after tissue homogenization (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocols. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Total RNA was then reverse transcribed followed by second strand cDNA synthesis. An in vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion, Austin TX). 1.5µg biotin-labeled cRNA was hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.
Label biotin
Label protocol Standard Illumina hybridization protocol
 
Hybridization protocol Standard Illumina scanning protocol
Scan protocol Probe set data, mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package
Description HFD: biological replicate 4
Data processing log2 transformation quantile normalization
 
Submission date Apr 24, 2009
Last update date Jan 21, 2010
Contact name Rachael S Hageman
E-mail(s) rachael.hageman@jax.org
Phone 216-906-2306
URL http://rachael.hageman@jax.org
Organization name The Jackson Laboratory
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL6105
Series (1)
GSE15822 High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice

Data table header descriptions
ID_REF
VALUE log2 transformation and quantile normalization

Data table
ID_REF VALUE
ILMN_1243094 7.231605744
ILMN_1240307 7.157387213
ILMN_2486639 7.408764492
ILMN_1229397 7.446259422
ILMN_1225873 8.596542684
ILMN_1231752 7.185454828
ILMN_1257702 12.45238996
ILMN_1251148 7.251989944
ILMN_2691286 7.236638992
ILMN_1213242 7.288724415
ILMN_2728484 7.103166875
ILMN_2748584 10.28607684
ILMN_2519069 7.557850985
ILMN_1213815 7.033084845
ILMN_1237075 13.4886697
ILMN_2649966 14.99391377
ILMN_2699167 12.03937215
ILMN_2586958 7.936588809
ILMN_2760075 7.823477263
ILMN_1255729 7.638591922

Total number of rows: 46632

Table truncated, full table size 1133 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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