|
| Status |
Public on Mar 22, 2012 |
| Title |
ZR-75-30-BMP4/vehicle-24h |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ZR-75-30 human breast cancer cell line, treated with vehicle, 24 h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ZR-75-30
agent: vehicle
time point: 24 h
|
| Biomaterial provider |
All the cell lines were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the recommended conditions.
|
| Treatment protocol |
Cells were seeded on 24-well plates, allowed to adhere for 24h, and treated with vehicle for 30min, 1h, 3h, 6h, 12h and 24h. Experiments were performed in triplicate and collected cells were pooled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) and the quality of RNA was validated using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (500 ng) was used to generate fluorescent Cy-3-(vehicle treated cells) or Cy-5-labeled cRNA (BMP4-treated cells) using the Agilent Low RNA Input Fluorescence Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
ZR-75-30 human breast cancer cell line, treated with BMP4, 24 h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ZR-75-30
agent: BMP4
time point: 24 h
|
| Biomaterial provider |
All the cell lines were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the recommended conditions.
|
| Treatment protocol |
Cells were seeded on 24-well plates, allowed to adhere for 24h, and treated with recombinant human BMP4 protein for 30min, 1h, 3h, 6h, 12h and 24h. Experiments were performed in triplicate and collected cells were pooled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) and the quality of RNA was validated using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA, USA).
|
| Label |
Cy5
|
| Label protocol |
Total RNA (500 ng) was used to generate fluorescent Cy-3-(vehicle treated cells) or Cy-5-labeled cRNA (BMP4-treated cells) using the Agilent Low RNA Input Fluorescence Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
The labeled cRNAs were hybridized to the 44K Whole Human Genome oligo microarrays (Agilent Technologies) according to the manufacturer’s protocol.
|
| Scan protocol |
Microarray slides were scanned (Agilent Microarray Scanner) after hybridization, and data were extracted using the Feature Extraction software, version A.7.5.1 (Agilent Technologies).
|
| Data processing |
Data were subjected to linear normalization to allow comparison between arrays. The normalized ratio data was obtained with the software named Anduril (version 1.1.0).
|
| |
|
| Submission date |
Aug 23, 2011 |
| Last update date |
Mar 24, 2012 |
| Contact name |
Alejandra Rodriguez-Martinez |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tampere
|
| Department |
Institute of Biomedical Technology
|
| Street address |
Biokatu 6
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL6480 |
| Series (2) |
| GSE31603 |
Human breast cancer cell lines: vehicle vs. BMP4 incubation |
| GSE31605 |
Human breast cancer cell lines |
|
