|
| Status |
Public on Feb 28, 2011 |
| Title |
patient 116, cancer, LCM [OPG study] |
| Sample type |
RNA |
| |
|
| Source name |
surgically resected material
|
| Organism |
Homo sapiens |
| Characteristics |
metastasis: none
stage: 2b
tissue: cancer, LCM
|
| Treatment protocol |
Tumor tissue was extracted using laser-capture microdissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue specimens using RNeasy kit (Qiagen, Hilden, Germany). Integrity of obtained RNA was assessed using Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA). All samples had RNA Integrity Number (RIN) greater than 5.0. Contaminant DNA was removed by digestion with RNase-free DNase (Qiagen).
|
| Label |
biotin
|
| Label protocol |
cRNA was prepared using two-cycle target labeling and control reagents kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) was performed following the manufacturer's instruction using the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression profile of surgically resected material
C116
|
| Data processing |
The data was normalized by robust multichip analysis (RMA) using R/Bioconductor (affy package).
|
| |
|
| Submission date |
Apr 26, 2010 |
| Last update date |
Feb 28, 2011 |
| Contact name |
Kaoru Mogushi |
| E-mail(s) |
mogushi-k@umin.ac.jp
|
| Phone |
+81-3-5802-1797
|
| Organization name |
Juntendo University
|
| Department |
Intractable Disease Research Center
|
| Street address |
2-1-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8421 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE21510 |
Clinical Significance of Osteoprotegerin Expression in Human Colorectal Cancer |
|
| Relations |
| Reanalysis of |
GSM452561 |
