|
| Status |
Public on Jun 01, 2010 |
| Title |
histologically normal breast epithelium from ER- breast cancer patient sample 2 |
| Sample type |
RNA |
| |
|
| Source name |
Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Organism |
Homo sapiens |
| Characteristics |
specimen: ER- Breast Cancer
disease state: breast cancer
tissue: breast epithelium
|
| Treatment protocol |
Tissues were snap frozen, embedded in OCT, sectioned at 10μm, stained with diluted hematoxylin and eosin (H&E) and then NlEpi – both TDLUs and ducts - was microdissected. Most HN samples were “tumor-adjacent” (i.e., located 1-2 cm from the tumor, on blocks lacking malignant cells. Some HN lay further away, but still in the same quadrant as the tumor, since most surgeries were lumpectomies. Great care was taken to avoid microdissecting any proliferative cells, even simple hyperplastic lesions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the microdissected cells using the PicoPure extraction kit (Molecular Devices, Sunnyvale, CA).
|
| Label |
Biotin
|
| Label protocol |
T7-based RNA amplification was performed on 100 ng of RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
10 µg of fragmented cRNA and hybridization controls were hybridized to each U133A GeneChip (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
|
| Scan protocol |
The stained arrays were scanned using a G2500 Scanner (Agilent)
|
| Description |
Gene Expression data from case 289H:Histologically Normal Epithelium from ER- Breast Cancer Patient
|
| Data processing |
.cel files were processed with MAS 5.0 using standard procedures for quality control and normalization was limited to rescaling each sample to a mean intensity of 200.
|
| |
|
| Submission date |
Feb 19, 2010 |
| Last update date |
May 31, 2013 |
| Contact name |
Kelly Graham |
| Organization name |
Boston University School of Medicine
|
| Department |
Hematology/Oncology
|
| Lab |
Rosenberg
|
| Street address |
650 Albany Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE20437 |
Histologically normal epithelium from breast cancer patients and cancer-free prophylactic mastectomy patients |
| GSE21947 |
Gene expression profiles of breast cancer subtypes are detectable in histologically normal breast epithelium |
|
| Relations |
| Reanalyzed by |
GSE47561 |
