Global proteomic analysis of WT and GRN-/- HeLa cells
By savannah onGlobal proteomic analysis of WT and GRN-/- HeLa cells. https://www.nature.com/articles/s41467-022-33500-9
Global lipidomics of WT and GRN-/- cells & mouse models, including plus and minus GRN addback
By savannah onThis 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)
By savannah onCryo-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
RAB3 phosphorylation by pathogenic LRRK2 impairs trafficking of synaptic vesicle precursors
By savannah onFor 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.
Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore: Molecular dynamics simulation data
By savannah onAtomistic 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 cells
By savannah onDataset 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.
Sex-specific microglial responses to glucocerebrosidase inhibition
By savannah onMorpho-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 disease
By savannah onAuxilin 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.
Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center
By savannah onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.
Images of adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain
By savannah onCAP-Mac, neuron-biased in infant Old-World primates, is shown to have potential for non-invasive systemic gene transfer in the brains of NHPs.
Single cell transcriptomics from DAT-Cre mouse gut tissue
By savannah onColonic myenteric cells were dissociated, and live tdTomato-positive cells were FACS-collected. Colons were isolated from 2 male and female wild type adult DAT-Cre mice. Wild type C57Bl6/J was used as control for gating. Cells were processed according to 10X Genomics Chromium single cell 3' Reagent guidelines.
circRNA dataset
By savannah onNew data set on circRNA in laser-captured neuron samples from 190 human brains of healthy controls, prodromal PD, and clinical PD (Dong et al., Nature Communications, in press). The RNA-seq raw FASTQ data and normalized expression matrix of all circRNAs in this study have been deposited in GEO under accession number GSE218203.
Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics
By savannah onThis dataset includes experimental data used to constrain and validate the model and model simulation output data in the Cell Reports publication: Dura-Bernal et al., 2023, "Multiscale model of primary motor cortex circuits predicts in vivo cell type-specific, behavioral state-dependent dynamics."
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
By savannah onGenomic sequences with high sequence similarity, such as parent-pseudogene pairs, cause short sequencing reads to align to multiple locations, thus complicating genomic analyses. However, their impact on transcriptomic analyses, including the estimation of gene expression and transcript annotation, has been less studied. The authors investigated the impact of pseudogenes on transcriptomic analyses.
Structure of human ULK1 complex core (2:1:1 stoichiometry)
By savannah onOrganism(s): Homo sapiens Expression System: Homo sapiens Mutation(s): No Deposited: 2023-04-28 Released: 2023-06-21 Deposition Author(s): Chen, M., Hurley, J.H. Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Structure of human PI3KC3-C1 complex
By savannah onOrganism(s): Homo sapiens Expression System: Homo sapiens Mutation(s): No Deposited: 2023-04-29 Released: 2023-06-21 Deposition Author(s): Chen, M., Hurley, J.H. Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Structure of human ULK1C:PI3KC3-C1 supercomplex
By savannah onOrganism(s): Homo sapiens Expression System: Homo sapiens Mutation(s): No Deposited: 2023-05-05 Released: 2023-06-21 Deposition Author(s): Chen, M., Hurley, J.H. Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
By savannah onOrganism(s): Homo sapiens Expression System: Homo sapiens Mutation(s): No Deposited: 2023-05-04 Released: 2023-06-21 Deposition Author(s): Chen, M., Hurley, J.H. Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Structure of human ULK1 complex core (2:2:2 stoichiometry) of the ATG13(450-517) mutant
By savannah onOrganism(s): Homo sapiens Expression System: Homo sapiens Mutation(s): No Deposited: 2023-05-05 Released: 2023-06-21 Deposition Author(s): Chen, M., Hurley, J.H. Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michael J. Fox Foundation
Metabolomic and lipidomic data reported in doi.org/10.1073/pnas.2219953120 (Golgi-IP, a tool for multimodal analysis of Golgi molecular content)
By savannah onMetabolomic and lipidomic data associated with doi.org/10.1073/pnas.2219953120 deposited in MetaboLights repository with identifier number MTBLS6511.