Raw band intensity values for ATG3 WT or Mutants in vitro LC3 lipidation
By Emma Sherrell onRaw band intensity values used for the quantification of in vitro LC3 lipidation results (Fig4C) in Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore.
Raw band intensity values for Halo-LC3B
By Emma Sherrell onRaw band intensity values used for the quantification of percentage autophagy levels.
Proteome of R1441C and G2019S LRRK2 knock in mice after striatal motor learning task
By Julia Julia Leonard onTo identify the signaling pathways that underlie the motor learning deficits, specifically in the RC mice, the authors performed six-plex tandem mass tag (TMT) quantitative mass spectrometry (MS) to compare the protein expression of either RC or GS and WT mice following the five days of the rotarod test.
Tabular data of fast-scanning voltammetry and physiology experiments in LRRK2 KI mice
By Julia Julia Leonard onThe tabular data of fast-scanning cyclic voltammetry and physiology experiments from manuscript: "R1441C and G2019S LRRK2 knockin mice have distinct striatal molecular, physiological, and behavioral alterations." by Xenias et al.
Tabular data of striatal motor learning experiments in LRRK2 KI mice
By Julia Julia Leonard onThe 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."
Tandem Mass Tag (TMT) label-based mass spectrometry analysis of RILPL1 interactors
By Julia Julia Leonard onPrimary 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
Mass spectrometry analysis of proteome changes in VPS35-WT vs VPS35[D620N] MEFs and VPS35[D620N] MEFs vs LRRK2 inhibitor in whole cell lysates and lysosomes
By Julia Julia Leonard onPrimary 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.
In vivo reduction of age-dependent neuromelanin accumulation mitigates features of Parkinson’s disease
By savannah onCollection 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”)
By Emma Sherrell onPrimary 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").
Next-generation sequencing of AAV.CAP-Mac enrichment from Chuapoco et al. (2023)
By Emma Sherrell onDataset 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
Jensen_etal_2022_molecular_dynamics_simulation_data_2
By Emma Sherrell onFull 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.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 2
By Emma Sherrell onPart 2 of NGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 1
By Emma Sherrell onNGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt
By Emma Sherrell onThis 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”
By Emma Sherrell onThis 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)
By savannah onRaw 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 for PD patients and controls from the BioCollective
By savannah onFecal metagenomic sequencing data associated with Boktor et al., 2023. This dataset includes samples from the BioCollective cohort.
Proteomics of iNeurons or HeLa cells with or without FBXO7
By savannah onTMT 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 neurons
By savannah onRaw 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
Membrane interaction and mechanism of LC3 lipidation machinery in autophagy – Raw GUV data
By savannah onRaw 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.