To study the impact of the geometric configuration of Figure 5 on resolution, Section 4.2 considers the target to be an isotropic point.
Of the 251 putative anchor genes selected, 200 were analysed using high resolution section in situ hybridisation (SISH) of paraffin-embedded E15.5 murine kidney.
The binding probability at each base pair location is achieved by integrating out all other locations (see 'Binding probabilities at single nucleotide resolution' Section more details).
In the study presented here, we have extended the analysis of the kidney development gene atlas using high resolution section in situ hybridisation (SISH).
Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high resolution section in situ hybridisation performed on 200 transcripts selected as specific to one of 11 anatomical compartments within the midgestation mouse kidney.
Although some high resolution section analyses with mouse tissues are not sufficient for providing global views, high similarities in the expressions of the orthologous genes in zebrafish and mouse were observed (Table S2).
The decreased sensitivity of the spp methods on the GABP dataset may be caused by the broader enrichment regions noted in this dataset (see Figures S6, S7 and S8 and further discussion in the "Spatial Resolution" section).
Moreover, calculating the spatial resolution (Section 2), the four methods show the largest agreement for the PR dataset, whereas USeq shows the lowest spatial resolution on NRSF, CEBPA and CTCF (Supplementary Fig. S12).
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