9 protocols
AccessionType
bioassay_data_transformation
Data was log2 transformed
bioassay_data_transformation
Data was background substracted and LOESS normalized using R (2.15)/Bioconductor/Limma
image_acquisition
Slides were scanned using an Agilent DNA Microarray Scanner G2505C; scan software: Agilent Scan Control Version A.8.1.3; quantification software: Agilent Feature Extraction Version 10.5.1.1 (FE Protocol GE_105_Dec08).(Parameters: Scanning hardware = G2505A DNA microarray scanner [Agilent], Scanning software = Feature Extraction Software [Agilent])
hybridization
Agilent Two-Color Microarray-Based Gene Expression (Hybridization)
Version: 5.7
Agilent publication number: G4140-90050
URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf
This document describes Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based two-color gene expression analysis.
pool
A equal aliquot of all Cy3 labeled extracts was pooled to build a reference.
labeling
Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling)
Version: 5.7
Agilent publication number: G4140-90050
URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf
This document describes Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based two-color gene expression analysis.
nucleic_acid_extraction
RNA was isolated using the Nucleospin RNA II kit (Macherey-Nagel, Dueren, Germany) according to manufacturers instructions.
compound_based_treatment
MDA-MB-231 cells were seeded at a density of 5x10^5 cells per 10 cm dish in 10 ml RPMI with 10% FCS and cultured in the presence of 0.3 micromolar GW501516 or DMSO as control (1:10.000) as solvent control. Treatment of the cells was repeated every 24h and cells were processed for RNA-analysis after 48h.
grow
MDA-MB-231 cells were obtained from ATCC and cultured in RPMI (PAA) supplemented with 10% fetal bovine serum, in a humidified incubator at 37 degrees Celcius and 5% CO2.