|
| Status |
Public on Apr 22, 2008 |
| Title |
Patient 13 |
| Sample type |
RNA |
| |
|
| Source name |
Patient 13 appendix
|
| Organism |
Homo sapiens |
| Characteristics |
appendix sample removed from patient who went to the operating room with the diagnosis of acute appendicitis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A 2.0 arrrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
A circumferential piece of tissue was obtained at the distal aspect of each specimen. The tissue was flash frozen at -80 degrees for later processing. Frozen specimens were homogenized into TriReagent and RNA was isolated according to the manufacturer’s instruction. RNA was processed and hybridized to Affymetrix microarray.
|
| Data processing |
The 13 data sets were first processed by Affymetrix GCOS V.1.4.0.036 software which computed present/absent calls for each probe set and the signal values were adjusted to an overall target intensity of 1500. Data was then normalized in Genespring version 7.3.1 in 3 steps. 1. Data trasnformation: set measurements less than 0.01 to 0.01. 2. per chip: Normalization to 50th percentile. 3. Per Gene: Normalize to median.
|
| |
|
| Submission date |
Nov 09, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Bruce H Horwitz |
| E-mail(s) |
bhorwitz@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital
|
| Street address |
77 Avenue Louis Pasteur
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE9579 |
Gene Expression in Acute Appendicitis |
|
