|
| 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 |
|
