|
| Status |
Public on Nov 10, 2011 |
| Title |
blood_patient 21 |
| Sample type |
RNA |
| |
|
| Source name |
blood_patient_single VTE
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
race: caucasian
age: 70
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extract from Paxgene Blood RNA tubes using the PAXgene Blood RNA Kit per the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Biotinylated antisense strand cRNA was prepared according to the standard Affymetrix protocol from 2.5 ug total RNA utilizing peptide nucleic acids complimentary to globin mRNA to block amplification of those transcripts(GeneChip® 1 cycle labeling kit with Globin Reduction protocol (Affymetrix) Data was Generated at Expression Analysis, Inc (Durham, NC))
|
| |
|
| Hybridization protocol |
20 ug of antisense cRNA was hybridized for 16+ hr at 45C on GeneChip Human U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Midi_euk2v3_450 protocol
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 7G
|
| Description |
none
|
| Data processing |
A comprehensive quality control process was performed on all arrays using Bioconductor. In addition to evaluating the standard quality control measures provided by Affymetrix, a series of graphical illustrations (e.g. boxplots of perfect match intensities, density histograms, raw and corrected chip images, MA plots, median absolute deviation plots, and multidimensional scaling plots) were produced and evaluated. Also, residual plots from probe-linear models were used to identify blemishes and defects on each chip. The expressions from the arrays were normalized using Robust Multichip Averaging pre-processing algorithm, and log (base 2) transformed (RMAExpress Version: 1.0 Release).
|
| |
|
| Submission date |
Nov 23, 2009 |
| Last update date |
Nov 10, 2011 |
| Contact name |
Thomas L. Ortel |
| E-mail(s) |
Thomas.Ortel@duke.edu, Deborah.Lewis@duke.edu
|
| Phone |
919 684 5350
|
| Fax |
919 681 6160
|
| URL |
http://htc.medicine.duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Hematology
|
| Street address |
Box 3422 DUMC
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE19151 |
Whole Blood Gene Expression Profiles Distinguish Patients with Single versus Recurrent Venous Thromboembolism |
|
