DOI: 10.5061/dryad.s7h44j1hw
title: Data from: Characterization of direct Purkinje cell outputs to the brainstem

description: Purkinje cells (PCs) primarily project to cerebellar nuclei but also
 directly innervate the brainstem. Some PC-brainstem projections have been
 described previously, but most have not been thoroughly characterized.
 Here we use a PC-specific cre line to anatomically and
 electrophysiologically characterize PC projections to the brainstem. PC
 synapses are surprisingly widespread, with the highest densities found in
 the vestibular and parabrachial nuclei. However, there are pronounced
 regional differences in synaptic densities within both the vestibular and
 parabrachial nuclei. Large optogenetically-evoked PC-IPSCs are
 preferentially observed in subregions with the highest densities of PC
 synapses, suggesting that PCs selectively influence these areas and the
 behaviors they regulate. Unexpectedly, the pontine central gray and nearby
 subnuclei also contained a low density of PC synapses, and large PC-IPSCs
 are observed in a small fraction of cells. We combined
 electrophysiological recordings with immunohistochemistry to assess the
 molecular identities of these PC targets. PC synapses onto mesencephalic
 trigeminal neurons were not observed even though these cells are in close
 proximity to PC boutons. PC synapses onto locus coeruleus neurons are
 exceedingly rare or absent, even though previous studies concluded that
 PCs are a major input to these neurons. The availability of a highly
 selective cre line for PCs allowed us to study functional synapses, while
 avoiding complications that can accompany the use of viral approaches. We
 conclude that PCs directly innervate numerous brainstem nuclei, but only
 inhibit a small fraction of cells in many nuclei. This suggests that PCs
 target cell types with specific behavioral roles in brainstem regions.
description: # Data from: Characterization of direct Purkinje cell outputs to the
 brainstem
 [https://doi.org/10.5061/dryad.s7h44j1hw](https://doi.org/10.5061/dryad.s7h44j1hw) ## Description of the data and file structure This data set are example images and analysis used in the published work, "Characterization of direct Purkinje cell outputs to the brainstem eLife 13:RP101825" [https://doi.org/10.7554/eLife.101825.1](https://doi.org/10.7554/eLife.101825.1) ### Files and variables #### File: figure1\_slidescanner.zip **Description:**  * raw images used for figure 1 * sorted by file name, coronal slides are named posterior to anterior, sagittal slices are named lateral to medial #### File: code\_dir.zip **Description:**  * analysis scripts for figure 2-4 - excel tables are exports from arivis vgat putative synapse location * put raw confocal images (see below) into the same directory as the rest of code_dir to run ‘fig2_colocalization.m’ - this script takes vat location data and synaptophysin confocal data and calculate colocalization * 'fig2_colocalization.m’ is a matlab script takes vat location data in excel and synaptophysin confocal data in raw tiff files and calculate colocalization * ’fig3_ephys_plot.m’ is a matlab script that takes variable from ‘figure3_ephys_varaible.mat’ and plot cell response amplitude on allen atlas outlines. * ‘figure3_ephys_varaible.mat’ is a matlab variable file that include two structure variable, each corresponding to cell location and cell amplitude. * ’fig4_ephys_plot.m’ is a matlab script that takes variable from ‘figure4_ephys_varaible_LC.mat’ and plot cell response amplitude on allen atlas outlines.  * ‘figure4_ephys_varaible_LC.mat’ is a matlab variable file that include two structure variable, each corresponding to cell location and cell amplitude.  * ‘masterslice’ is a directory that contain jpg files of allen atlas outlines of the dorsal brainstem at bregma -5.65mm, -6.05mm, -6.35mm, -6.65mm #### File: Sld1slc12-left-TileScan\_1\_Region\_2\_Merged\_z00\_ch03.tif #### File: Sld2slc1-TileScan\_1\_Region\_1\_Merged\_z00\_ch03.tif #### File: Sld3Slc8-Region\_2\_Merged\_RAW\_ch03.tif #### File: Sld2slc8-TileScan\_6\_Region\_1\_Merged\_z00\_ch03.tif #### File: Sld3Slc2-Slide3\_101722\_Region\_3\_Merged\_z00\_ch03.tif #### File: Sld3Slc11-TileScan\_1\_Region\_5\_Merged\_z00\_ch03.tif * The above list of raw syanptophysin channel confocal image stack used for figure 2 colocalization analysis #### File: sld1slc12\_multiCh.tif #### File: sld3slc8\_\_multiCh.tif  #### File: sld2slc1\_\_multiCh.tif #### File: sld2slc8\_\_multiCh.tif #### File: sld3slc11\_multiCH\_ch04.tif #### File: sld3sld2\_multiCh\_ch04.tif list of raw synaptophysin channel and vat channel confocal image that generated vGAT location using ZEISS arivis