|
| Status |
Public on Mar 11, 2011 |
| Title |
P056M |
| Sample type |
RNA |
| |
|
| Source name |
Pretherapeutic rectal cancer patient biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: P056
disease status: rectal cancer
age: 67.9
gender: male
tissue: mucosa
genome/variation: mutated KRAS
|
| Treatment protocol |
No treatment prior to expression profiling analysis was performed.
|
| Growth protocol |
Biospies from patients not cell lines were used for analyses
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies were immediately stored in RNAlater (Qiagen, Hilden, Germany). Subsequently, RNA and DNA was isolated using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer´s instructions. Nucleic acid quantity, quality and purity were determined using a spectrophotometer (Nanodrop, Rockland, DE) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
1 µg of total RNA was labeled with Cy3 using the Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's recommendations (Agilent Technologies, Santa Clara, CA). Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.
|
| |
|
| Hybridization protocol |
1.5 mg of Cy3-labeled cRNA was hybridized to an oligonucleotide-based Whole Human Genome Microarray (4x44K, Agilent Technologies) and incubated at 65˚C for 17 hours.
|
| Scan protocol |
Slides were washed and scanned using an Agilent G2565BA scanner.
|
| Description |
Human pretherapeutic rectal cancer patient biopsy sample P056M
|
| Data processing |
Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.
|
| |
|
| Submission date |
Mar 11, 2010 |
| Last update date |
Jun 27, 2011 |
| Contact name |
Marian Grade |
| E-mail(s) |
marian.grade@gmail.com
|
| Organization name |
University Medical Center Goettingen, Georg-August-University
|
| Department |
Surgery
|
| Street address |
Robert-Koch-Str. 40
|
| City |
Goettingen |
| ZIP/Postal code |
37075 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE20842 |
Mutated KRAS induces overexpression of DUSP4, a MAP-kinase phosphatase, and SMYD3, a histone methyltransferase, in rectal carcinomas |
|
