|
| Status |
Public on Mar 01, 2007 |
| Title |
CD-33-Aff |
| Sample type |
RNA |
| |
|
| Source name |
colonoscopic biopsy from adult with affected colon with Crohn's disease
|
| Organism |
Homo sapiens |
| Characteristics |
disease affected colon of an adult with Crohn's disease (CD).
|
| Treatment protocol |
Fresh biopsy was placed on ice in the Trizol solution (Invitrogen).
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45oC on GeneChip U95Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner (Affymetrix).
|
| Description |
Colonic biopsy was collected during endoscopy from affected area of a patient with Crohn's disease. The standard Affymetrix protocols were followed to prepare target from 5ug of total RNA. The expression profiles generated from normal individuals were compared to that from patients with different types of disease.
|
| Data processing |
The DNA-Chip Analyzer (dChip) software (Li, C. and Wong, W.H. 2001) was used to normalize the image data and calculate the expression value.
|
| |
|
| Submission date |
Jan 16, 2007 |
| Last update date |
Mar 16, 2009 |
| Contact name |
Shukti Chakravarti |
| E-mail(s) |
[email protected]
|
| Phone |
410-502-7627
|
| Fax |
410-614-4834
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Medicine
|
| Lab |
935 Ross Bldg/ GI division
|
| Street address |
720 Rutland Ave
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL8300 |
| Series (1) |
| GSE6731 |
Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies: |
|
