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Nested primers for amplification of bisulfite converted DNA (Additional file 13) were designed using MethPrimer [ 89] and the sequencing data analyzed using BiQ analyzer [ 90].
Cells were then analyzed using a LSRFortessa cell analyzer (BD Biosciences), and data analyzed using FlowJo version 7.6.4 software.
Analysis was performed using a Fortessa analyzer (Beckman Coulter, High Wycombe, UK) and data analyzed using FlowJo v7.6.5 (Ashland, OR).
Flow cytometry was performed using MACSQuant Analyzer (Miltenyi Biotec, U2OS cells) and FACSAria (Beckton Dickinson, S2 cells), and data analyzed using Bioconductor package flowCore.
Data analyzed using Crimson Hexagon are proprietary and are not publicly available.
An Introduction to Exposure Maps (PS, 12pp) gives a comparison of MARX simulated data analyzed using both weighted and monochromatic exposure maps.
We combined these with TCGA raw count data analyzed using the same pipeline and compiled a transcriptomic dataset comprising of 1558 healthy normal samples, 428 NAT samples, and 4500 primary tumor samples across eight tissue types (Table 1).
Data analyzed using SPSS-windows.
Data analyzed using the FlowJo software v7.6.1.
All data analyzed using GraphPad Prism 5.0 software (San Diego, CA, USA).
Data analyzed using one-way ANOVA on ranks and multiple comparisons were adjusted using the Dunn's method.
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