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Sample GSM195559 Query DataSets for GSM195559
Status Public on Jun 13, 2007
Title Adipose Pool vs Adipose_Sample_201
Sample type RNA
 
Channel 1
Source name Adipose
Organism Homo sapiens
Characteristics Adipose Pool
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 Adipose
Organism Homo sapiens
Characteristics Adipose_Sample_201
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 The genetics of human gene expression from population based tissue sampling
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 May 30, 2007
Last update date Jun 13, 2007
Contact name Valur Emilsson
E-mail(s) valur_emilsson@merck.com
Organization name Merck
Department Genetics
Street address 401 Terry Avenue N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL3991
Series (1)
GSE7965 Blood and Adipose tissue samples

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE Corrected Log10 Ratio of channels (CH2/CH1)
LOGINTENSITY Corrected average log intensity of channels
INTENSITY1 Cy3 intensity (CH1)
INTENSITY2 Cy5 intensity (CH2)
PVALUE P-value of LogRatio
QUALITY 1 - if good and non control, 0 - otherwise

Data table
ID_REF VALUE LOGINTENSITY INTENSITY1 INTENSITY2 PVALUE QUALITY
10019475365 -0.1519 -0.5583 0.3294 0.2322 2.3241e-001 1
10019481149 0.2012 -0.2016 0.4986 0.7924 1.1712e-001 1
10019495284 -0.0576 -0.5047 0.3343 0.2928 6.4320e-001 1
10019687586 0.1068 -1.4236 0.0333 0.0426 5.6247e-001 1
10019713746 -0.1365 -0.7359 0.2149 0.1570 2.8699e-001 1
10019799479 -0.0857 -1.1126 0.0852 0.0699 5.4049e-001 1
10019809115 -0.3149 -0.6787 0.3011 0.1459 2.2107e-002 1
10019874890 -0.0190 -1.1450 0.0732 0.0701 8.9363e-001 1
10019909307 0.4463 -0.2315 0.3510 0.9810 2.5480e-003 1
10019911222 -0.0262 -0.8625 0.1414 0.1331 8.3800e-001 1
10019924807 0.1160 -0.5932 0.2232 0.2916 3.5762e-001 1
10019927856 -0.2979 -0.0545 1.2430 0.6260 2.6769e-002 1
10019932383 0.1141 -0.5541 0.2448 0.3184 3.6441e-001 1
10019948931 0.1188 -1.1843 0.0571 0.0750 4.1868e-001 1
10019975533 0.0196 -1.1787 0.0648 0.0678 8.9216e-001 1
10019977227 -0.0011 0.7291 5.3657 5.3520 9.9280e-001 1
10019987588 0.2035 -0.8678 0.1073 0.1714 1.2742e-001 1
10020008603 0.0524 -1.0570 0.0826 0.0932 6.9991e-001 1
10020014121 0.2991 -0.4057 0.2785 0.5544 2.6722e-002 1
10020044367 -0.0274 -0.8134 0.1586 0.1489 8.2907e-001 1

Total number of rows: 23653

Table truncated, full table size 1276 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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