|
| Status |
Public on Jan 01, 2017 |
| Title |
Responder - sample 53 |
| Sample type |
RNA |
| |
|
| Source name |
Pre Treatment biopsies
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CRC sample
disease state: Rectal cancer
name: E113
age: 63
Sex: Male
class: Responder
|
| Treatment protocol |
Pre CRT research biopsies (2-3 mm3) were collected during the initial diagnostic endoscopy, immediately frozen and stored in a liquid nitrogen tank.
|
| Growth protocol |
No growth protocols were used
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by phenol/chloroform extraction (TRIzol; Invitrogen) prior to further purification by column chromatography (RNeasy Mini kit; Qiagen). RNA integrity was then assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies)
|
| Label |
biotin
|
| Label protocol |
Agilent Whole Human Genome GE44K microarray platform was used. Standard Agilent RNA extraction and hybridization protocols were used.
|
| |
|
| Hybridization protocol |
Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.
|
| Scan protocol |
Arrays were scanned using the Agilent Scanner G2505B
|
| Description |
Gene expression data from CRC patients at diagnosis
|
| Data processing |
The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] "Agi4x44PreProcess" (intra-array[Multiplicatively Detrended] and inter-array [Quantile] normalization).
|
| |
|
| Submission date |
Mar 21, 2013 |
| Last update date |
Jan 01, 2017 |
| Contact name |
Andrea Zangrando |
| E-mail(s) |
andrea.zangrando@unipd.it
|
| Organization name |
University of Padova
|
| Department |
Woman and Child's Health
|
| Lab |
Hemato-Oncology
|
| Street address |
Via Giustiniani, 3
|
| City |
Padova |
| ZIP/Postal code |
35138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE45404 |
Integrative computational biology and molecular determinants of rectal cancer resistance to chemoradiotherapies |
|
