|
| Status |
Public on Oct 01, 2011 |
| Title |
CE11-001-OCT-Carotid-Section-03 |
| Sample type |
RNA |
| |
|
| Source name |
carotid plaque
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: carotid plaque
patient: CE11-001
sample id: CE11-001-OCT-Carotid-Section-03
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
|
| Label protocol |
The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45?C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
Gene expression profiling of carotid plaque. 6 subjects from OCT6 study. Plaques were sectioned in 1 mm slices. Half of the slices were profiled, and the other half, adjacent slices, were processed by IHC
|
| Data processing |
Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://bioinformatics.oxfordjournals.org/cgi/content/full/22/9/1111).
|
| |
|
| Submission date |
Oct 04, 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 |
GPL10687 |
| Series (2) |
| GSE23314 |
Gene expression profiling of human atherosclerotic plaque |
| GSE24495 |
Gene expression profiling of human atherosclerotic plaque: Carotid plaque |
|
