|
| Status |
Public on Dec 10, 2010 |
| Title |
breast_cancer_T5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
biopsy and surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
disease state: cancer
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
polyA RNA were purified from four (N1 to N4) normal organoid and four breast tumor samples as described previously (PMID: 17349583).
|
| Label |
Cy5
|
| Label protocol |
Two hundred nanograms of mRNA was directly labeled with Cy3 using a ULS micro-RNA labeling kit (Kreatech) and fragmented with an RNA fragmentation kit (Ambion). For the reference sample, equal amounts of mRNA from the four normal samples were mixed together, labeled with Cy5.
|
| |
|
| Channel 2 |
| Source name |
pooled polyA RNA from four normal organids from reduction mammoplasty
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast
disease state: normal
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
polyA RNA were purified from four (N1 to N4) normal organoid and four breast tumor samples as described previously (PMID: 17349583).
|
| Label |
Cy3
|
| Label protocol |
Two hundred nanograms of mRNA was directly labeled with Cy3 using a ULS micro-RNA labeling kit (Kreatech) and fragmented with an RNA fragmentation kit (Ambion). For the reference sample, equal amounts of mRNA from the four normal samples were mixed together, labeled with Cy5.
|
| |
|
| |
| Hybridization protocol |
For each individual array, 200 ng of Cy3-labeled normal or tumor sample was mixed with 200 ng of Cy5-labeled reference sample and twocolor hybridization was performed according to the manufacturer's protocol (Agilent Technologies).
|
| Scan protocol |
Image analysis was conducted using Agilent Feature extraction software (version 10.5.1.1; Agilent Technologies)
|
| Data processing |
Image analysis was conducted using Agilent Feature extraction software (version 10.5.1.1; Agilent Technologies), and processed signals and LogRatio were used for further analysis. To confirm the presence of antisense transcripts, a rigorous threshold was applied using the flag IsWellAboveBG.
|
| |
|
| Submission date |
Dec 10, 2010 |
| Last update date |
Dec 13, 2010 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL11305 |
| Series (2) |
| GSE25292 |
Altered antisense-to-sense transcript ratios in breast cancer |
| GSE26000 |
Altered antisense-to-sense transcript ratios in breast cancer: Agilent |
|
