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\title {\textbf{Supplementary Information}

Circadian disruption coincides with morphological changes in the suprachiasmatic nucleus in a genetic $\alpha$-synuclein rat model of early Parkinson's disease}

\author[1]{Hanna Weber, Meike Statz, Nicolas Casadei, Olaf Riess, Franziska Richter, Wiebke Hermann, Alexander Storch, Mareike Fauser}


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\section*{List of supplementary information}

\textbf{Supplementary figure 1:} Tyrosine hydroxylase (TH) DAB-Staining in the \textit{substantia nigra} (SN) and ventral tegmental area (VTA) of wild-type (WT) and $\alpha$-synuclein expressing rats (SNCA).

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\noindent\textbf{Supplementary figure 2:} Heatmap showing Pearson correlation coefficients between corrected $\alpha$-synuclein immunoreactivity and cellular parameters in the suprachiasmatic nucleus (SCN).




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\caption{\label{korrelation} \textbf{Tyrosine hydroxylase (TH) DAB-Staining in the \textit{substantia nigra} (SN) and ventral tegmental area (VTA) of wild-type (WT) and $\alpha$-synuclein expressing rats (SNCA).}  
\textbf{(a)} Representative TH stainings of the SN and VTA of WT and SNCA rats. Scale bar = 1,000~µM.    
\textbf{(b)} Magnifications of representative TH stainings of the SN and VTA of WT and SNCA rats. Scale bar~=~100~µM.
\textbf{(a)} Representative TH stainings of the dorsal striatum (STRd), \textit{Nucleus accumbens core} region (NACC), and the anterior commissure (ACO). Scalbar~=~1,000~µM.   
\textbf{(d)} Quantification of TH-positive neurons in the SN. No significant differences were observed between groups.  
\textbf{(e)} Quantification of TH-positive neurons in the VTA without significant group differences.
\textbf{(f)} Quantification of TH-positive fibers in the dorsal striatum did not reveal any group differences.
\textbf{(g)} Quantification of TH-positive fibers in the vetrnal striatum. No significant differences were detected between groups.
Data are presented as boxplots with median (central line), interquartile range (box), and minimum/maximum values (whiskers). Individual data points are shown as dots.
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\begin{figure}[t]
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\includegraphics[width=0.7\linewidth]{Supplementary_Information_2.png}
\caption{\label{korrelation} \textbf{Heatmap showing Pearson correlation coefficients between corrected $\alpha$-synuclein immunoreactivity and cellular measures in the suprachiasmatic nucleus (SCN).}
Columns represent wild-type (WT; left) and $\alpha$-synuclein expressing rats (SNCA; right), and rows depict cell or fiber counts (N/mm\textsuperscript{3}) for Hoechst, Iba1, Orexin A, NeuN, vasopressin (VP), and vasoactive intestinal peptide (VIP) cells/fibers (top), as well as percentages relative to total Hoechst\textsuperscript{+} cells for Iba1, Orexin A, NeuN, VP, and VIP (bottom). In WT rats, correlations are negligible due to the absence of detectable $\alpha$-synuclein, whereas SNCA rats show uniformly positive correlations, with significant correlations between $\alpha$-synuclein intensity and Iba1\textsuperscript{+} cells and Orexin A\textsuperscript{+} fibers, respectively. Color intensity represents the magnitude of the correlation coefficient (Pearson r; *$p<0.05$, **$p<0.01$).}
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