Proteomic and functional data sets on synaptic mitochondria from rats with genetic ablation of Parkin

In this paper, we provide proteomic and functional data for synaptic mitochondria from the striatum of rats with Parkin ablation. The quantitative proteomic data was obtained using SWATH-MS methodology and mitochondrial function was assessed through measurement of oxygen consumption rate using the Seahorse XF Analyzer. This data facilitates comparisons with previous proteomic and functional data obtained using the exact same methods. A complete set of proteomic data is contained in Supplementary Table 1.


a b s t r a c t
In this paper, we provide proteomic and functional data for synaptic mitochondria from the striatum of rats with Parkin ablation. The quantitative proteomic data was obtained using SWATH-MS methodology and mitochondrial function was assessed through measurement of oxygen consumption rate using the Seahorse XF Analyzer. This data facilitates comparisons with previous proteomic and functional data obtained using the exact same methods. A complete set of proteomic data is contained in Supplementary

Value of the data
These data sets provide a useful resource to identify different synaptic mitochondrial processes that are affected due to loss of Parkin.
This data will aid in comparisons of synaptic mitochondrial changes in Parkin KO rats with other PD animal models.

Data
Bioenergetic data generated using the Seahorse XF e 96 Extracellular Flux Analyzer is provided. No significant alteration of either the respiratory state ( Fig. 1A) or the electron transport chain function ( Fig. 1B) for striatal synaptic mitochondria from 3-month-old male Parkin KO rats was found. Furthermore, no significant alteration was present in either the amount of proton leak (Fig. 1C) or the respiratory control ratio (RCR, Fig. 1D), which is an overall measure of mitochondrial health.
SWATH-MS-based proteomic data is presented for striatal synaptic mitochondria from 3-monthold Parkin KO rats, compared to control animals. The list of 131 differentially expressed proteins is provided in Supplementary Table 1. Consistently changed proteins found from the comparison of the striatal synaptic and non-synaptic mitochondria [1] isolated from Parkin KO rats are shown in Table 1. Furthermore, common differentially expressed proteins in striatal synaptic mitochondria from Parkin KO and PINK1 KO rats [2] are shown in Table 2.

Animals
Male Long Evans Hooded (LEH) (RRID:RGD_2308852) control and Parkin KO rats [3] were used at 3 months of age (three rats from each strain for respiration studies, n ¼ 3; and four rats from each strain for proteomic experiments, n ¼ 4). All protocols were conducted within NIH-approved guidelines for the Care and Use of Laboratory Animals with the approval and oversight of the University of Nebraska Medical Center Institutional Animal Care and Use Committee.

Isolation of synaptic mitochondria and respiration analysis
Brains were rapidly isolated from the animals, and the striatum (identified as per [4]) was removed by an investigator blinded to rat genotype and immediately rinsed with ice-cold 1x Phosphate Buffered Saline (Sigma, 806552) to remove blood. Tissue was chopped and homogenized using 10 strokes with a Dounce homogenizer (abcam, ab110169). Striatal synaptic mitochondria were isolated as previously described [5] with slight modifications [6] and oxygen consumption rates were measured using 3-4 technical replicate wells (7.5 μg of striatal synaptic mitochondria per well) for each biological replicate with a Seahorse XFe24 Analyzer (Agilent) for the previously described coupling and electron flow assays [7]. For data calculation the Seahorse Wave software (v2.2.0) was used. Prism (GraphPad) was used for graphs and statistical analyses (ANOVA and Sidak's multiple comparisons post-hoc testing).

Sample preparation for mass spectrometry
Synaptic mitochondria were lysed in 4% sodium dodecyl sulfate (Gibco, 15553), protein concentration was determined using a Pierce 660 nm Protein Assay (Thermo Fisher Scientific, 22660), and the filter aided sample preparation method [8] was used to prepare the synaptic mitochondrial peptides for mass spectrometry as described previously [9]. Table 1 Differentially expressed proteins in both striatal non-synaptic and synaptic mitochondria from Parkin KO compared to control rats. Protein expression values listed are log 2 (Parkin KO/LEH). List of striatal non-synaptic mitochondrial proteins significantly altered in Parkin KO rats obtained from previously published work [1].

Funding
Funding support was provided by a grant from the Michael J Fox Foundation (Grant #9524).

Transparency document. Supporting information
Transparency data associated with this article can be found in the online version at https://doi.org/ 10.1016/j.dib.2018.08.053.

Appendix A. Supporting information
Supplementary data associated with this article can be found in the online version at https://doi. org/10.1016/j.dib.2018.08.053.