For each stain, the fluorescent signals were observed in the expected cell type(s) and subcellular distributions, with minimal cross-talk between channels.
Therefore, we utilized a novel statistical method to infer expected cell type fractions in our study samples based on a validated subset of methylation markers as a surrogate measure (Houseman et al. 2012); the assumptions of the statistical method have been described elsewhere (Koestler et al. 2013a, 2013b).
The manufacturer indicates that it specifically detects Cx45 in mouse brain homogenates in western blots and stains expected cell types in retina and mouse brain.
Jarid2 activity, a known repressor with an essential role in embryonic development, was enriched in expected cell types, such as undifferentiated ESCs and induced pluripotent stem cells (Supplementary Fig. S2A; Landiera and Fisher, 2011).
In Stuart et al. (2004) linear regression models, regressing expression on fractional content of tumor (or stroma), were used to estimate the expected cell-type expression as the regression coefficient.
However, as we do expect cell types to have a discrete biological basis, we might expect our model to do well with real data.
As expected, cell lines with wild-type TP53 responded to Nutlin-3a exposure by activation of p53 and its downstream targets, including p21 and MDM2, whereas tumours with mutated TP53, irrespective of mutation site, did not respond to Nutlin-3a alone.
Neurolucida analysis of the confocal image stack acquired at ∼48 hpf provided separate, continuous traces of CaP, MiP and RoP that conformed to the expected cell-specific morphology of each cell type (Fig. 1E) (Eisen et al., 1986; Myers et al., 1986; Westerfield et al., 1986).
We expect each cell type to have a unique transcriptome [ 24].
As expected, both cell types exhibited selective clonal proliferation in the recipient liver.
As expected, all cell types were highly present in alveolar space after bleomycin instillation, with the highest increase in number of lymphocytes and neutrophils.
