|
| Status |
Public on Dec 31, 2012 |
| Title |
Stable Plaque, biological rep 5 |
| Sample type |
RNA |
| |
|
| Source name |
Macrophages, LMDed from Stable Carotid Atheromatous Plaque
|
| Organism |
Homo sapiens |
| Characteristics |
age: 68
gender: female
days from last symptom: n/a
symptom event: N/A
radiological stenosis: 95.0 (%)
plaque histology: Stable Thick Fibrous Cap Atheroma
cell type: macrophage
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen RNeasy Micro kit. RNA quality and quantity was assessed by RIN score using the RNA6000 Pico Labchip (Agilent Bioanalyser 2100, Agilent). Only samples with RIN scores of 6 and above were considered suitable for microarray analysis.
|
| Label |
Biotin
|
| Label protocol |
Twenty to sixty nanograms of total RNA were subjected to two cycles of linear amplification using the Affymetrix GeneChip Two-Cycle Target Labeling Kit.
|
| |
|
| Hybridization protocol |
Standard Affymetrix Protocol using the GeneChip Two-Cycle Target Labelling Kit
|
| Scan protocol |
Standard Affymetrix protocols using the Affymetrix 3000 GeneChip Scanner and GCOS ver.1.3 to generate RAW probe data in .cel files.
|
| Description |
Gene expression data from macrophages isolated from stable plaques of Asymptomatic patients
|
| Data processing |
The RAW microarray data were analyzed using the GeneSpring GX 7.3.1 analysis package. Raw microarray signal data were pre-processed and normalized using GCRMA, and normalised to the median. Affymetrix external control probesets and probesets that were called absent in more than 6 of the 11 samples and were prefiltered out. The resulting 25538 of the 54675 probesets were analysed using ANOVA with corrections for the error of multiple testing by the Benjamini and Hochberg method.
RAW values in matrix file were the log transformed GCRMA processed signal intensity values. NORMALIZED values in the matrix file were the ratios of the log transformed GCRMA processed signal intensity values to the median. The ABS_CALL were the absent and present calls generated by the standard Affymetrix algorithm using GCOS ver.1.3 without any alteration from the default value of Tau. File matrix_NORMALIZED_RAW_ABSCALL.txt is linked as a supplementary file on the Series record.
|
| |
|
| Submission date |
Oct 14, 2012 |
| Last update date |
Dec 31, 2012 |
| Contact name |
Kelvin Lee |
| E-mail(s) |
kelvinlee726@me.com
|
| Organization name |
Institute of Genetic Medicine, University of Newcastle upon Tyne
|
| Department |
Cardiovascular Research
|
| Street address |
International Centre for Life, Central Parkway
|
| City |
Newcastle upon Tyne |
| State/province |
Tyne and Wear |
| ZIP/Postal code |
NE1 3BZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE41571 |
Genome-wide expression profiling of laser micro-dissected macrophages from ruptured and stable atherosclerotic human plaques |
|
