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Sample GSM321017 Query DataSets for GSM321017
Status Public on Aug 10, 2009
Title f2#57 versus pool Mouse Muscle tissue
Sample type RNA
 
Channel 1
Source name #57
Organism Mus musculus
Characteristics Strain:C57BL/6J and C3H/HeJ Age:20 weeks Gender:Male
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy spin columns with DNAse treatment
Label Cy3
Label protocol custom automated version of the aminoallyl MessageAmp II kit from Ambion
 
Channel 2
Source name pool
Organism Mus musculus
Characteristics Strain:C57BL/6J and C3H/HeJ Age:24 weeks (150 randomly selected F2)
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy spin columns with DNAse treatment
Label Cy5
Label protocol custom automated version of the aminoallyl MessageAmp II kit from Ambion
 
 
Hybridization protocol Microarrays are incubated at 40°C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.
Scan protocol Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software
Description Muscle tissue from 285 F2 female and male mice were fed chow diet containing 4% fat (Ralston-Purina Co., St. Louis, MO) until 8 weeks of age and then were placed on a high-fat "Western" diet containing 42% fat and 0.15% cholesterol (Teklad 88137, Harlan Teklad, Madison WI) for 12 weeks. At 20 weeks mice were sacrificed, after a 12-hour fast, Muscle tissue were dissected and flash frozen in LN2 and stored at -80°C. All sample were compared to a common pool created from equal portions of RNA from each of the samples.
Data processing Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.
 
Submission date Sep 16, 2008
Last update date Aug 10, 2009
Contact name Leslie Ingram-drake
E-mail(s) lingram@mednet.ucla.edu
Phone 310-794-9036
Fax 310-794-7345
URL http://www.mednet.ucla.edu
Organization name UCLA
Department Medicine/MIMG/Human Genetics
Street address 47-123 CHS
City Los Angeles
State/province CA
ZIP/Postal code 90095-1359
Country USA
 
Platform ID GPL2510
Series (1)
GSE12795 Expression profiling of Muscle tissue from C57BL/6J X C3H/HeJ)F2 and (C3H/HeJ X C57BL/6J)F2

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE MLRATIO: Averaged log10 ratio [log10(CHANNEL1/CHANNEL2 ), error weighted]
PVALUE P-value derived from the error model for expression differences between the two channels, as described in He YD et al,Bioinformatics. 2003 May 22;19(8):956-65
INTENSITY1 Cy3 intensity (CH1)
INTENSITY2 Cy5 intensity (CH2)

Data table
ID_REF VALUE PVALUE INTENSITY1 INTENSITY2
10024393144 1.4316842425614595E-3 0.97702533006668091 0.20493 0.20516999999999999
10024393145 7.5667782220989466E-4 0.9883887767791748 0.56498999999999999 0.55974000000000002
10024393146 -5.5740000680088997E-3 0.96382516622543335 1.9081999999999999 1.8838999999999999
10024393147 6.7804604768753052E-3 0.91487103700637817 0.10766000000000001 0.10825
10024393148 -0.11371669173240662 5.4362021386623383E-2 0.1804 0.13805000000000001
10024393149 2.6786472648382187E-2 0.63058829307556152 0.28366999999999998 0.30202000000000001
10024393150 -0.14169473946094513 7.4541340582072735E-3 1.8795999999999999 1.3567
10024393151 -1.3796847779303789E-3 0.99205470085144043 4.7684999999999998E-2 0.047895
10024393152 7.8850656747817993E-2 0.75566530227661133 0.010765 1.2239999999999999E-2
10024393153 5.8686710894107819E-2 0.27666193246841431 2.2565 2.5903
10024393154 2.4229466915130615E-2 0.64994311332702637 0.29405999999999999 0.31403999999999999
10024393155 2.0748842507600784E-4 0.99828189611434937 4.0099999999999997E-2 0.040075
10024393156 3.3087190240621567E-2 0.51712197065353394 0.22919 0.24732999999999999
10024393157 4.8018068075180054E-2 0.31005463004112244 1.228 1.3727
10024393158 -8.3650358021259308E-2 0.12175461649894714 1.9957 1.6515
10024393159 -1.0258249938488007E-2 0.83143657445907593 2.706 2.6423999999999999
10024393160 2.7516830712556839E-2 0.71226042509078979 5.2034999999999998E-2 5.5559999999999998E-2
10024393161 -6.0871397145092487E-3 0.92714077234268188 0.11074000000000001 0.10897999999999999
10024393162 4.2215164750814438E-2 0.41199153661727905 0.37633 0.41541
10024393163 0.21237687766551971 0.57738304138183594 0.005855 8.6800000000000002E-3

Total number of rows: 23524

Table truncated, full table size 2040 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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