6 protocols
AccessionNameType
P-GSE49858-1
normalization data transformation protocol
The Agilent Feature Extraction Software (FES 10.5.1.1 ) was used to read out and process the microarray image files. ID_REF = VALUE = median normalized signal intensities
P-GSE49858-6
array scanning protocol
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).
P-GSE49858-5
hybridization protocol
Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays (44K) using Agilent’s recommended hybridization chamber and oven.Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.
P-GSE49858-4
labelling protocol
1 µg of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.
P-GSE49858-3
nucleic acid extraction protocol
RNA was prepared using standard RNA extraction protocols (Trizol). Quality was checked via the Agilent 2100 Bioanalyzer platform.
P-GSE49858-2
sample treatment protocol
Human immortalized mesenchymal stromal cells (SCP-1) were incubated with conditioned medium of the breast carcinoma cell line MCF-7 for 24, 48, and 72 hours at 37 ºC in a humidified incubator with 5% CO2.