|
| Status |
Public on Dec 05, 2013 |
| Title |
breast_invasive ductal carcinoma_8013 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
breast_invasive ductal carcinoma_8013
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age at diagnosis: 76
treatment type: exemestane
age at start therapy: 79
menopausal status at start therapy: post
tissue: breast
tumor type: invasive ductal carcinoma
location: breast
grade: 2
er status: positive
pr status: positive
her2 status: negative
pik3ca status: wildtype
disease-free interval (months): 36
disease relapse (event): 1
time-to-progession (months): 30
disease progression (event): 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
A reference sample was made by processing of a breast cancer reference pool (BRP) (previously generated by pooling breast tumor RNAs [Glas et al, BMC Genomics 2006]) similarly as the testsamples.
|
| Label |
Cy3
|
| Label protocol |
Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]
|
| |
|
| Channel 2 |
| Source name |
common breast cancer reference pool (BRP)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
A reference sample was made by processing of a breast cancer reference pool (BRP) (previously generated by pooling breast tumor RNAs [Glas et al, BMC Genomics 2006]) similarly as the testsamples.
|
| Label |
Cy5
|
| Label protocol |
Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf]
|
| |
|
| |
| Hybridization protocol |
Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner
|
| Data processing |
Raw Green (ch1, sample) and Red (ch2, reference) expression levels were quantified using Agilent Feature Extraction software (version 9.5) based on MedianSignal output. Expression levels were normalized by lowess normalization using standard Feature expression software settings (see manual for details at http://www.chem.agilent.com/Library/usermanuals/Public/ReferenceGuide_050416.pdf).
|
| |
|
| Submission date |
Nov 01, 2012 |
| Last update date |
Mar 03, 2016 |
| Contact name |
Paul Roepman |
| Organization name |
Agendia
|
| Street address |
Science Park 406
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16233 |
| Series (1) |
| GSE41994 |
Expression profiling of response to first-line aromatase inhibitor therapy |
|
| Relations |
| Affiliated with |
GSM2079921 |
