Dataset Archive

Atomistic molecular dynamics simulation data set accompanying manuscript, "Three-step docking by WIPI2, ATG16L1 and ATG3 delivers LC3 to the phagophore.”

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.

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.

Fecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.

CAP-Mac, neuron-biased in infant Old-World primates, is shown to have potential for non-invasive systemic gene transfer in the brains of NHPs.

Colonic 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.

New 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.

This 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."

Genomic 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.

Organism(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

Organism(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

Organism(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

Organism(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

Organism(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 associated with doi.org/10.1073/pnas.2219953120 deposited in MetaboLights repository with identifier number MTBLS6511.

A platform to view integrated data from the Wade-Martins Laboratory of Molecular Neurodegeneration. Results and data from Kilfeather, Khoo, et al. 2023 (Manuscript in review): Spatial Transcriptomic Analyses: -Cell Type Markers -SN/VTA Markers in Dopaminergic Neurons -Cell Number Changes in Age TRAP Analyses: -Dopaminergic Markers -Dopaminergic Aging -Alternative Splicing in Dopaminergic Neurons

Raw data reported in Supplementary table in "Whole Proteome Copy Number Dataset in Primary Mouse Cortical Neurons."

The bands for each subunit of the PI3KC3-C1 complex (VPS15, VPS34, ATG14, and Beclin1) were extracted from the gel and submitted for mass spectrometry analysis.

This work reveals that OPTN mitophagy initiation is mechanistically distinct and highlights the mechanistic plasticity of selective autophagy pathways.