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Sample GSM397512 Query DataSets for GSM397512
Status Public on Mar 31, 2010
Title GonadalFat.HFD.5
Sample type RNA
 
Source name Gonadal Fat: HFD
Organism Mus musculus
Characteristics strain: DBA/2J
tissue: Gonadal 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 5
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 7.331901958
ILMN_1240307 7.162161375
ILMN_2486639 7.451239506
ILMN_1229397 7.444494563
ILMN_1225873 8.149401274
ILMN_1231752 7.32763905
ILMN_1257702 12.39103152
ILMN_1251148 7.163394746
ILMN_2691286 7.138776887
ILMN_1213242 7.128050568
ILMN_2728484 6.98935936
ILMN_2748584 10.13054526
ILMN_2519069 7.616698973
ILMN_1213815 6.94244417
ILMN_1237075 13.14307337
ILMN_2649966 14.80003609
ILMN_2699167 11.95264865
ILMN_2586958 7.917463674
ILMN_2760075 7.857937992
ILMN_1255729 7.502689452

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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