For the PCR array, the RT2 Profiler Stem Cell PCR Array (catalog number PAHS-405; SuperArray, Frederick, MD, USA) was used according to the manufacturer's protocol.
Cell profiler software [17] allows users to combine image-processing methods to develop techniques to count cells, but this requires some knowledge of computation and it has not been tested for specific applications.
Data analysis for in situ PLA images was performed using the freeware Cell Profiler, developed by the Broad Institute ( http://www.cellprofiler.org ).org
Foci were quantified by manual counting and the Cell Profiler Software (www.cellprofiler.org).org
Images were analysed using Cell Profiler [27] to identify DAPI labelled nuclei by Otsu thresholding, and measure the intensity of OCT4 and NANOG immunolabelling in the detected areas.
Nuclei were counted with Cell Profiler (Carpenter et al., 2006).
The Cell Profiler pipeline developed for this study is provided as a.cp file (Supplementary file 1).
Cell profiler (Broad Institute, [ 20]) was used for automated analysis of images.
Neighbor analysis was performed with Cell Profiler [ 32] from fluorescence images.
The number of cells and the GFPLC3 cluster in the cells were quantified using Cell Profiler software.
