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Sample GSM571577 Query DataSets for GSM571577
Status Public on Oct 01, 2011
Title LCM_SmoothMuscle_Seg1 vs. (n=9) cRNA reference pool
Sample type RNA
 
Channel 1
Source name Peripheral plaque
Organism Homo sapiens
Characteristics sample type: (n=9) cRNA reference pool
tissue: whole carotid plaques from 9 samples
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 Peripheral plaque
Organism Homo sapiens
Characteristics tissue: carotid plaque from smooth muscle cell rich section
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 Gene expression profiling of peripheral plaque. Laser Capture Microscopy of smooth muscle cell-rich regions and macrophage-rich regions from carotid plaque sections. Profiled in the Merck/Agilent 44k v1.1
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 Jul 28, 2010
Last update date Oct 01, 2011
Contact name Oscar Puig
E-mail(s) oscar_puig@merck.com
Organization name Merck Research Laboratories
Department Molecular Profiling Research Informatics
Street address 126 East Lincoln Ave
City Rahway
State/province NJ
ZIP/Postal code 07065
Country USA
 
Platform ID GPL4372
Series (2)
GSE23303 Gene expression profiling of human atherosclerotic plaque: Laser capture microscopy of smooth muscle cells and macrophages
GSE23314 Gene expression profiling of human atherosclerotic plaque

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 0.0746 -0.6398 0.2126 0.2541 1.5582e-001 1
10019481149 0.0563 -0.5579 0.2624 0.2979 2.4368e-001 1
10019495284 -0.2983 -1.1779 0.0941 0.0473 7.1024e-008 1
10019687586 -0.0301 -1.5796 0.0275 0.0257 6.6430e-001 1
10019713746 0.1128 -0.5395 0.2580 0.3345 1.1331e-002 1
10019799479 0.0907 -0.6893 0.1842 0.2271 8.5745e-002 1
10019809115 0.2203 0.2022 1.2431 2.0565 4.1846e-004 1
10019874890 0.0826 -0.6773 0.1912 0.2312 9.0926e-002 1
10019903058 -0.0510 -2.3961 0.0070 0.0055 9.2528e-001 1
10019909307 0.0402 -0.9457 0.1110 0.1222 4.2127e-001 1
10019911222 -0.0471 -0.8921 0.1361 0.1232 4.4692e-001 1
10019924807 0.0697 -0.5584 0.2551 0.3018 2.9017e-001 1
10019927856 0.1528 0.7308 4.5118 6.4144 2.2525e-001 1
10019932383 -0.1004 -0.5212 0.3383 0.2693 9.1840e-002 1
10019948931 0.5212 -0.7408 0.0996 0.3328 2.7031e-013 1
10019975533 0.4705 -0.3580 0.2563 0.7573 1.2221e-018 1
10019977224 -0.1486 -0.7486 0.2120 0.1512 1.8527e-002 1
10019977227 -0.0278 0.8738 7.8187 7.2592 7.7038e-001 1
10019987588 0.0838 -0.5862 0.2362 0.2873 1.0086e-001 1
10020008603 0.0589 -0.6445 0.2144 0.2453 1.9204e-001 1

Total number of rows: 39096

Table truncated, full table size 2108 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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