19 protocols
AccessionNameType
P-GSE42071-19
feature_extraction
Statistical analysis of the data was performed using the lumi package for Bioconductor/R (www.r-project.org)
P-GSE42071-16
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.
P-GSE42071-15
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.
P-GSE42071-10
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 =
P-GSE42071-18
image_aquisition
Chips were scanned according to the manufacturer’s instructions and the scanner output imported into BeadStudio software (Illumina, Cambridge, UK)
P-GSE42071-17
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)
P-GSE42071-14
grow
CHRF288-11 cells were cultured in RPMI 1640, 10% fetal calf serum, 2 mM l-glutamine in a humidified incubator with 5% CO2
P-GSE42071-8
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 =
P-GSE42071-13
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
P-GSE42071-7
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 =
P-GSE42071-6
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 =
P-GSE42071-5
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 =
P-GSE42071-2
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 =
P-GSE42071-1
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 =
P-GSE42071-9
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 =
P-GSE42071-3
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 =
P-GSE42071-11
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 =
P-GSE42071-12
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 =
P-GSE42071-4
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 =