|
| Status |
Public on Feb 04, 2010 |
| Title |
patient 113, cancer, LCM |
| Sample type |
RNA |
| |
|
| Source name |
surgically resected material
|
| Organism |
Homo sapiens |
| Characteristics |
metastasis: metastasis
tissue: cancer, LCM
|
| Treatment protocol |
Tumor tissues were extracted using laser-capture microdissection for 77 samples. Homogenized tissues were used for 17 pairs of cancer and non-cancerous tissues.
|
| 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
|
| Data processing |
The data was normalized by robust multichip analysis (RMA) using R/Bioconductor. Normalization was performed separately for LCM samples and homogenized samples.
|
| |
|
| Submission date |
Sep 14, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Kaoru Mogushi |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE18105 |
Stage II and stage III colorectal cancer |
|
| Relations |
| Reanalyzed by |
GSM537340 |
| Reanalyzed by |
GSM687480 |
| Reanalyzed by |
GSE119087 |
