Dataset Archive

The tabular data of the behavioral experiments described in the manuscript titled, "R1441C and G2019S LRRK2 knockin mice have distinct striatal molecular, physiological, and behavioral alterations."

Primary mass spectrometry data associated with Fig.5 in the manuscript, "Parkinson’s VPS35 mutation induces LRRK2 mediated lysosomal association of RILPL1 and TMEM55B" (Association of RILPL1 with a lysosomal membrane integral protein, TMEM55B mediated by LRRK2 activity). Curtain link for the dataset: https://curtain.proteo.info/#/4f15d6c8-9192-4bb2-a2ff-da7aa542025c

Primary mass spectrometry data associated with Fig.1 and Fig.2 in the manuscript "Parkinson’s VPS35 mutation induces LRRK2 mediated lysosomal association of RILPL1 and TMEM55B" (Phospho-Rab and RILPL1 enrichment at VPS35 mutant lysosome and Lysosomal recruitment of RILPL1 is dependent on LRRK2 kinase activity). Curtain links for the datasets: https://curtain.proteo.info/#/0e673d58-d8f2-4368-996b-0869d5513d46; https://curtain.proteo.info/#/0e673d58-d8f2-4368-996b-0869d5513d46; https://curtain.proteo.info/#/d864df78-e2a5-4a64-99fb-8c5d8b2e1ab8; https://curtain.proteo.info/#/062e0a64-1fd3-4cc1-833a-a5b007d95a3c.

Collection of all datasets (Metabolomics, microscopy, and behavioral data) included in the article entitled "In vivo reduction of age-dependent neuromelanin accumulation mitigates features of Parkinson’s disease."

Primary data associated with the manuscript 10.1073/pnas.2315171120 ("Localization of PPM1H phosphatase tunes Parkinson’s disease-linked LRRK2 kinase-mediated Rab GTPase phosphorylation and ciliogenesis").

Dataset of next-generation sequencing of enrichment of AAV.CAP-Mac in various tissues from the publication: Chuapoco, M.R., Flytzanis, N.C., Goeden, N. et al. Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. Nat. Nanotechnol. (2023). https://doi.org/10.1038/s41565-023-01419-x

Full molecular dynamics simulation data set accompanying Jensen et al, 2022, containing (i) representative coordinates and measurements described therein, (ii) simulation trajectories, and (iii) GROMACS input files.

Part 2 of NGS data associated with Uoselis et al., 2023.

NGS data associated with Uoselis et al., 2023.

This study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.

This study demonstrates that the authors' semi-automated protocol is suitable for shotgun metagenomic analysis, by significantly producing higher DNA fragment sizes while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.

Raw immunoblotting data and their quantitation and graphs obtained using GraphPad Prism; PCR and sequencing data confirming that PPM1H-BromoTag clone E5 (used for all experiments in the manuscript) is a homozygous clone.

Fecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.

TMT proteomics datasets from FBXO7-/- hESC differentiation to iNeurons and HeLa cells.

Raw tomogram of a TauRD-YFP aggregate in a TauRD-YFP expressing Hek293T cells. Accession numbers: HEK293T: https://www.ebi.ac.uk/emdb/EMD-13739 Primary mouse neurons: https://www.ebi.ac.uk/emdb/EMD-13740

Raw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan 359 Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental 360 condition. Identical laser power and gain settings were used during the course of all conditions.

Global proteomic analysis of WT and GRN-/- HeLa cells. https://www.nature.com/articles/s41467-022-33500-9

This dataset contains: - Global lipidomics of WT and GRN-/- HeLa cells, including plus and minus GRN addback. - Global lipidomics of WT and NPC1-/- HeLa cells. - Global lipidomics of WT and GRN-/- HeLa cells, including plus and minus GRN addback. Global lipidomics of WT and GRN mutant mouse brain tissue. https://www.nature.com/articles/s41467-022-33500-9

Cryo-ET of S. cerevisiae during starvation (tomograms). Accession number: https://www.ebi.ac.uk/emdb/EMD-15526 https://www.ebi.ac.uk/emdb/EMD-15545 https://www.ebi.ac.uk/emdb/EMD-15546 https://www.ebi.ac.uk/emdb/EMD-15547 https://www.ebi.ac.uk/emdb/EMD-15549 https://www.ebi.ac.uk/emdb/EMD-15548

For quantitative results, gray cells represent breaks between independent experiments, or between individual fields of view. Please contact E.L.F. Holzbaur (corresponding author, [email protected]) with any questions or concerns.