|
| Status |
Public on Jan 07, 2013 |
| Title |
DMSO_5 |
| Sample type |
RNA |
| |
|
| Source name |
MCF-7 breast adenocarcinoma cells, control
|
| Organism |
Homo sapiens |
| Characteristics |
cell_line: MCF-7
cell_type: ER-positive breast adenocarcinoma cells
treatment: DMSO
treatment duration: 6hrs
replicate: 5
|
| Treatment protocol |
Cells were grown to 60% confluence, and then treated with Thiostrepton (10μM) or DMSO (0.1%) for 6 hr.
|
| Growth protocol |
The human MCF-7 cell line was obtained from the ECACC (European Collection of Animal Cell Cultures) and grown in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy kit (Qiagen) following the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
An aliquot of total RNA was run in triplicate on a NanoDrop spectrophotometer to determine sample concentration, and an aliquot of total RNA was run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality. Good-quality samples were normalised to 22.7ng/µl. 250ng of quality total RNA was processed following the Ambion Illumina® TotalPrep™-96 RNA Amplification Kit standard protocols.
|
| |
|
| Hybridization protocol |
An aliquot of cRNA was run in triplicate on a NanoDrop spectrophotometer to determine sample concentration and yield. Samples were normalised to 150ng/µl. An aliquot of normalised cRNA was run on an Agilent Bioanalyser RNA Nano capillary electrophoresis chip to determine quality. 750ng of labelled cRNA was hybridised to Illumina BeadArrays overnight, and BeadArrays were washed and stained with streptavidin-Cy3, following the Illumina WGGX DirectHyb Assay Guide (11286331 RevA).
|
| Scan protocol |
BeadArrays were scanned using the AutoLoader and BeadArray scanner at default settings following the BeadArray Reader User Guide (11179510 RevB). Metric files produced automatically save P95 and P05 readings and .xml files save scanner settings.
|
| Description |
5921992093_F
|
| Data processing |
Using the R beadarray package, the data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: Detection p-values are not available as the Bioconductor beadarray package was used to analyse raw bead-level data instead of the Illumina GenomeStudio software.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
Jan 07, 2013 |
| Contact name |
Dario Beraldi |
| E-mail(s) |
dario.beraldi@cruk.cam.ac.uk
|
| Organization name |
Cambridge Research Institute
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE40766 |
Genome-wide mapping of FOXM1 binding reveals co-binding with oestrogen receptor alpha in breast cancer cells (expression) |
| GSE40767 |
Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells |
|
