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”)on
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.
Feacal metagenomic data related to “Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics”on
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.
Primary data associated with the manuscript “CURTAIN – A Unique Web-based tool for exploration and sharing of MS-based proteomics data” (doi: https://doi.org/10.1101/2023.07.25.550405)on
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 and primary mouse neuronson
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, holzbaurpennmedicineupennedu) with any questions or concerns.
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation dataon
Atomistic molecular dynamics simulation data set accompanying manuscript, "Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore.”
Differential response of α-synuclein expression to bacterial ligands and metabolites in mouse enteroendocrine cellson
Dataset for manuscript, "α-synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells." Tabs in excel file are titled with the figure number.
Morpho-dynamic analysis occurring in primary cells derived from female and male mice in response to proinflammatory stimulations and glucocerebrosidase inhibition.
Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s diseaseon
Auxilin participates in clathrin uncoating to facilitate presynaptic endocytosis. This file contains the data set used to generate all the main figures of loss-of-function mutations of auxilin (PARK19 using KO mice, Vidyadhara et al., 2023 to show that synaptic vesicle sorting deficits, cytoplasmic dopamine accumulation, dopamine transporter mistrafficking, and synaptic autophagic.