|
Status |
Public on Feb 25, 2019 |
Title |
stool_P46_rep0 |
Sample type |
RNA |
|
|
Source name |
Stool sample; precancerous adenoma on colonoscopy
|
Organism |
Homo sapiens |
Characteristics |
tissue: Stool disease status: Adenoma Sex: Female age (yr): 54 ethnicity: Caucasian/white smoking status: No 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 |
27357 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 |
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