|
| Status |
Public on Mar 29, 2013 |
| Title |
IBC#12 (RNA) |
| Sample type |
RNA |
| |
|
| Source name |
IBC, core-biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: IBC
her2: 3+
er: 0
|
| Treatment protocol |
For tumor samples, 5–20 frozen sections of biopsy (16 μm thick) were manually microdissected. Under the guidance of a pathologist, normal tissue was removed leaving tumor cells comprising greater than 90% of the specimen. For normal breast samples, 40–60 frozen sections of surgical specimen (16 μm thick) were subjected for microdissection manually.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy micro kit (Qiagen; Valencia, CA, USA), and quality was characterized with BioAnalyzer (Agilent Technologies; Waldbronn, Germany).
|
| Label |
Cy3
|
| Label protocol |
RNA samples were labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Cy3-labelled cRNA was fragmented at 60°C for 30 minutes according to the manufacturer's instructions. On completion of the fragmentation reaction, 100 µl of fragmentation mixture were hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, XDR Lo 10%).
|
| Description |
Two technical replicates were integrated with mean.
|
| Data processing |
Extract tif images using the Feature Extraction software FE9.5 by GE1-v5_95 protocols. Normalization was performed using global-normalization methods. Two technical replicates were integrated with mean.
|
| |
|
| Submission date |
Mar 28, 2013 |
| Last update date |
Mar 29, 2013 |
| Contact name |
Takahiro Kogawa |
| E-mail(s) |
tkogawa1@mdanderson.org
|
| Organization name |
MD Anderson
|
| Department |
Breast Medical
|
| Street address |
1515 Holcomb Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE45581 |
Expression Analysis of Microdissected Inflammatory Breast Cancer |
| GSE45584 |
Expression Analysis and Genomic Analysis of Microdissected Inflammatory Breast Cancer |
|
