|
| Status |
Public on Feb 17, 2011 |
| Title |
Patient 446B DCIS (mRNA) |
| Sample type |
RNA |
| |
|
| Source name |
ductal carcinoma in situ epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: laser capture microdissected human breast
tissue: ductal carcinoma in situ epithelium
gender: female
age: 54 y
|
| Treatment protocol |
Primary patient breast tissue was snap-frozen in liquid nitrogen, embedded in optimal cutting temperature compound and stored at -80C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
On average, ~50 10 um-thick cryostat sections were prepared for the extraction of total RNA by laser-capture microdissection from normal or DCIS epithelial regions, which were identified by a surgical pathologist (AdlM) using every 7th section stained by Hematoxylin and Eosin. Total RNA was extracted from the captured epithelium using the Picopure RNA Isolation Kit (Arcturus Engineering) according to manufacturer's protocol with additional DNAse treatment step.
|
| Label |
biotin
|
| Label protocol |
To convert the RNA to cDNA, the purified total RNA was linearly amplified for two rounds using the MessageAMP aRNA Kit (Ambion, Austin, TX), in which the first round is based on an oligo-dT primer and T7 RNA polymerase. 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 446B ductal carcinoma in situ
|
| Data processing |
Images from the scanned chips were quantified and scaled using Affymetrix Microarray Suite 5.0 (Affymetrix), and the unnormalized data were then rescaled to a target of 100 to remove bias.
|
| |
|
| Submission date |
Oct 04, 2010 |
| Last update date |
Feb 18, 2011 |
| Contact name |
Bethany Hannafon |
| E-mail(s) |
hannafon@bu.edu, bethanyn_hannafon@dfci.harvard.edu
|
| Organization name |
Boston University School of Medicine
|
| Department |
Medicine/Section of Hematology and Oncology
|
| Lab |
Carol Rosenberg, M.D.
|
| Street address |
650 Albany Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE24506 |
Expression of microRNAs and their gene targets are dysregulated in pre-invasive breast cancer (mRNA) |
| GSE24509 |
Expression of microRNAs and their gene targets are dysregulated in pre-invasive breast cancer |
|
