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33P-labelled sense and antisense riboprobes were hybridized to serial parasagittal sections of additional (n = 4 6) adult male zebra finches followed by phosphorimager autoradiography (Typhoon 9410, GE Healthcare) for a global assessment of brain mRNA distribution, or emulsion autoradiography followed by Nissl (cresyl violet or toluidine blue) counterstaining for regional and cellular analysis.
Ruthenium red staining of sections of additional seeds derived from crosses of Col plants pollinated with Col and osd1 at 4 DAP and 6 DAP.
Another interesting aspect of this study is that a large number of the ChIP-Seq mapped CgrA binding sites did not affect neighboring gene expression (Fig. 2; white sections of Additional file 2: Table S2).
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Parameters used in the sGs procedure are available in A3 section of Additional file 1: Tables S6 and S7.
Base pairing for five individual sequences is shown in the middle section of Additional file 1.
(further information and derivations can be found in the "Model Derivation" section of Additional file 1).
AlzPathway is available as both the SBML map for CellDesigner (Additional file 1; see the section of Additional files) and the high resolution image map (Additional file 2; see the section of Additional files).
Instruction on how to access the AlzPathway web service (online map) is described in the Additional documentation file (Additional file 3; see the section of Additional files).
Due to computational constraints, we check a reduced version of the computational model (see the "Model Checking" section of Additional file 1 for details).
The dynamics described by (6-11) analogousgous to the reactions in (5), as shown in the "Model derivations" section of Additional file 1.
Table 1 summarises estimates of the model parameters based on values reported in the biological literature; these are discussed further in the "Biological Parameter Estimates" section of Additional file 1. Parameters used for both the stochastic and deterministic models.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com