19 protocols
AccessionType
feature_extraction
Statistical analysis of the data was performed using the lumi package for Bioconductor/R (www.r-project.org)
labeling
Total RNA (500 ng) was amplified using the Illumina Total Prep RNA Amplification Kit (Applied Biosystems, Warrington, UK) according to the manufacturer’s instructions.
nucleic_acid_extraction
Cells were collected as described above, lysed in 200 μL Trizol reagent (Invitrogen, Paisley, UK) and prepared according to the manufacturer’s instructions.
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_D =
image_aquisition
Chips were scanned according to the manufacturer’s instructions and the scanner output imported into BeadStudio software (Illumina, Cambridge, UK)
hybridization
The biotinylated cRNA (1500 ng per sample) was applied to Illumina HumanWG-6 v3 Expression BeadChips and hybridized overnight at 58˚C. Chips were washed, detected and scanned according to the manufacturer’s instructions and the scanner output imported into BeadStudio software (Illumina, Cambridge, UK)
grow
CHRF288-11 cells were cultured in RPMI 1640, 10% fetal calf serum, 2 mM l-glutamine in a humidified incubator with 5% CO2
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_B =
specified_biomaterial_action
For RNA preparation, cells (106/mL) were cultured in serum free medium for 16 hours before treatment with recombinant Wnt3a (150 ng/mL), Wnt5a (1200 ng/mL) or both Wnt3a and 5a in combination
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_A =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_F =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_E =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_B =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_A =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_C =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_C =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_E =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194088_F =
bioassay_data_transformation
ID_REF = VALUE = The data was preprocessed by Bioconductor lumi package (version 2.6.0). It was vst transformed and quantile normalized (log2 values are shown) Detection-4743194086_D =