|
| Status |
Public on Sep 01, 2013 |
| Title |
SW620_3 |
| Sample type |
RNA |
| |
|
| Source name |
human colorectal cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SW620
|
| Treatment protocol |
Cells are untreated. Sixty-nine hours after transfection, cells were exposed to 3µM of 5-FU and a single dose of 2 Gy of X-rays, and cell survival was determined by a standard colony formation assay.
|
| Growth protocol |
Cell lines were cultured in their recommended medium (Invitrogen, Karlsruhe, Germany), supplemented with fetal bovine serum (Pan, Aidenbach, Germany) and 2 mM L-glutamine (BioWhittaker, Verviers, Belgium).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each cell line, total RNA was isolated from three different passages (passage four to six, at 60-70% confluence) using the miRNeasy Mini kit (Qiagen), according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA and Spike-In were labeled by ligation to Cy3-conjugated 3´, 5´-cytidine-bisphosphate using T4 RNA ligase. Spin columns were used for desalting (BioRad, Hercules, CA, USA).
|
| |
|
| Hybridization protocol |
Hybridization was carried out for 20 hours.
|
| Scan protocol |
Slides were washed and scanned using an Agilent G2505B scanner.
|
| Data processing |
Raw data were extracted using the Feature Extraction software version 9.1 (Agilent Technologies). Median signal intensities from the Feature Extraction Software were converted to log2 and quantile normalized using the R package “limma”.
|
| |
|
| Submission date |
Sep 18, 2012 |
| Last update date |
May 20, 2014 |
| Contact name |
Frank Kramer |
| E-mail(s) |
frank.kramer@med.uni-goettingen.de
|
| Organization name |
University Medical Center Göttingen
|
| Department |
Department of Medical Statistics
|
| Street address |
Humboldtallee 32
|
| City |
Goettingen |
| ZIP/Postal code |
37073 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16770 |
| Series (1) |
| GSE40976 |
Identification of a microRNA expression signature for radiochemosensitivity of colorectal cancer cells, involving miRNAs-320a, -224, -132 and let7g |
|
