|
| Status |
Public on Feb 25, 2019 |
| Title |
stool_P25_rep0 |
| Sample type |
RNA |
| |
|
| Source name |
Stool sample; precancerous adenoma on colonoscopy
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Stool
disease status: Adenoma
Sex: Male
age (yr): 53
ethnicity: Caucasian/white
smoking status: Yes
family history: No
set: Training
|
| Treatment protocol |
Approximately 20 grams of stool were transferred to a 50mL conical tube with 30mL HBSS, 0.05% Tween-20, and 0.01% RNase inhibitor. Samples were rotated at 4 degrees Celsius for 10 minutes and solution was centrifuged at 500g for 10 minutes. Human cells were resuspended in lysis buffer.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total nucleic acid was extracted using the standard protocol on the bead-based Nucli-SENS easyMag.
|
| Label |
biotin
|
| Label protocol |
Total mRNA was prepared and labeled according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2017, Thermo Fisher Scientific).
|
| |
|
| Hybridization protocol |
Approximately 100ng of DNase-free RNA was amplified with the Ambio WT-pico kit with hybridization to the Affymetrix Human Transcriptome Array 2.0 as per the manufacturer's protocol.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner.
|
| Description |
27219 P
Transcriptome Expression Data
|
| Data processing |
The data was normalized using the Single Space Transformation-Robust Multiarray Analysis and analyzed using the Affymetrix Expression Console.
|
| |
|
| Submission date |
Jun 01, 2017 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Erica Kay Barnell |
| E-mail(s) |
e.barnell@wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
McDonnell Genome Institute
|
| Lab |
Griffith
|
| Street address |
4444 Forest Park
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63108 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE99573 |
Clinical Performance of a Stool RNA Assay for Early Detection of Precancerous Adenomas and Colorectal Cancer |
|
