|
| Status |
Public on Dec 28, 2016 |
| Title |
Patient IT126 |
| Sample type |
RNA |
| |
|
| Source name |
primary colorectal adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary colorectal adenocarcinoma
overall survival months from surgery date, last updated 02/01/2016: 109.96
vital status at the time of last follow up,2/1/2016: Alive
adjuvant chemoradiation or radiation therapy: no adjuvant chemoradiation or radiation reported
tumor grade: moderately differentiated
msi status summary based on combined ihc and molecular assay: MSS (including MSI-L)
tumor location: right side, left side or both: right
lympho-vascular invasion: Yes
age at diagnosis (years): 59
Sex: Female
simplified crc stage at diagnosis: Stage III
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Labbeling was done according to Nimblegen one color DNA Labeling kit.
|
| |
|
| Hybridization protocol |
Hybridization done according to Agilent Gene expression hybridization kit
|
| Scan protocol |
Scanned on Agilent SureScan Microarray Scanner (Agilent Technologies G2600D SG12434244)
|
| Data processing |
Data pre-processing steps of background-correction, normalization and summarization were performed in R using functions in Limma library. The raw intensity for each probe is the median feature pixel intensity with the median background subtracted. Data was quantile normalized followed by log2 transform. Signals from probes measuring same ncRNA were averaged.
|
| |
|
| Submission date |
Dec 27, 2016 |
| Last update date |
Dec 28, 2016 |
| Contact name |
Simone Anfossi |
| E-mail(s) |
SAnfossi@mdanderson.org
|
| Phone |
1-713-563-1323
|
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Experimental Therapeutics
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL22858 |
| Series (1) |
| GSE92928 |
ncRNA expression-based, individualized outcome prediction for CRC patients |
|
