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This data analysis environment is currently being developped further into a systematic mouse stem cell data analysis atlas (R. Kolde and J. Vilo, unpublished results).
To estimate residual sample contamination for monocyte and T cell data analysis, we generated separate enrichment scores for neutrophils, B cells, T cells, monocytes, and natural killer cells.
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A good review on bioinformatics tools useful for single-cell data analysis was published by Poirion et al. [72].
In this Primer, we provide an overview of available methods and discuss experimental design and single-cell data analysis.
Cell cycle data analysis was performed using the CELL-FIT software (Becton Dickinson, San Jose, CA, USA).
Clonal cell survival data analysis confirmed the synergistic effect of PCI of scFvMEL/rGel in the A-375 cells (data not shown).
Images from one cell are shown in Fig. 2. The brightfield image, (a), is used to define the outline of the cell for data analysis.
In contrast to the heterologous cell data, however, analysis of the EWS/FLI transcriptional profile in A673 Ewing's sarcoma cells revealed that the fusion protein downregulated more genes than it upregulated [8], [14], [15].
qPCR cycle threshold (Ct) raw data were processed with ViiA 7 RUO software (Life Technologies) excluding data that failed QC. miR-646 was removed from primary cell data set analysis, since mature miR-646 was not expressed in rat.
BZ participated in cell experiments, data analysis and writing manuscript.
Cell cycle data analysis was performed using Modfit LT software.
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