Primary data associated with the manuscript “Whole proteome copy number dataset in primary mouse cortical neurons” (doi: 10.1016/j.dib.2023.109336)
By onRaw data reported in Supplementary table in "Whole Proteome Copy Number Dataset in Primary Mouse Cortical Neurons."
Lentivirus production
By onThis protocol is associated with the following preprint, published on February 19, 2022: “The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds.”
Live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells
By onProtocol for live imaging to investigate mitophagy kinetics and NEMO recruitment in HeLa-M cells.
Gene editing of YIPF4 in hESCs V3
By onThis protocol describes the creation of YIPF4 knockout cell lines in H9 hESC cells using CRISPR-Cas9. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Microscopy-based bead protein-protein interaction assay
By onAn assay to study protein-protein interaction
Dopaminergic axons track somatic signaling in behaving mice
By onHere, authors used genetic strategies to isolate key dopaminergic neuron subtypes and monitor their axonal and somatic signaling patterns in behaving mice.
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
By onSelective autophagy is essential for maintaining cellular homeostasis. Using in vitro reconstitution, the authors explored the details of mitophagy initiation from autophagy receptor engagement through LC3 lipidation.
Raw tomogram of a TauRD-YFP aggregate in a TauRD-YFP expressing HEK293T cells and primary mouse neurons.
By 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
CRISPResso analysis
By onThis protocol describes the process of using CRISPResso to analyze Next Generation Sequencing (NGS) data from CRISPR-targeted, genome-edited samples.
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 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.
Stereotaxic Injections
By onStereotaxic injections for Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain.
Immunofluorescence of macrophages and microglia
By onThis protocol describes the fixation and staining of cultured cells in paraformaldehyde solution.
Disruption of lysosomal proteolysis in astrocytes facilitates midbrain proteostasis failure in an early-onset PD model
By onAccumulation of advanced glycation end products (AGEs) on biopolymers accompany cellular aging and drives poorly understood disease processes. Here, we studied how AGEs contribute to development of early on-set Parkinson’s Disease (PD) caused by loss-of-function of DJ1, a protein deglycase. In induced pluripotent stem cell (iPSC)-derived midbrain organoid models deficient for DJ1 activity, we find that lysosomal proteolysis is impaired, causing AGEs to accumulate, α-synuclein (α-syn) phosphorylation to increase, and proteins to aggregate. These processes are at least partly driven by astrocytes, as DJ1 loss reduces their capacity to provide metabolic support and triggers acquisition of a pro-inflammatory phenotype. Consistently, in co-cultures, we find that DJ1-expressing astrocytes are able to reverse the proteolysis deficits of DJ1 knockout midbrain neurons. In conclusion, astrocytes’ capacity to clear toxic damaged proteins is critical to preserve neuronal function and their dysfunction contributes to the neurodegeneration observed in PD.
Glucose Tolerance Test
By onThe glucose tolerance test is performed to determine how quickly the glucose is cleared from the blood. It is used to test for diabetes or insulin resistance.
Striatal Cannula Window Implantation
By onThis protocol describes how to implant a cannula window over the dorsolateral striatum in mice to enable two-photon imaging of dopamine axons in the dorsal striatum.
Workflow for proteomic analysis of purified lysosomes in cells lacking GRN V.3
By onAssociated with the following preprint (published September 30th 2021): Progranulin deficiency results in reduced bis(monoacylglycero)phosphate (BMP) levels and gangliosidosis Sebastian Boland, Sharan Swarup, Yohannes A. Ambaw, Ruth C. Richards, Alexander W. Fischer, Shubham Singh, Geetika Aggarwal, Salvatore Spina, Alissa L. Nana, Lea T. Grinberg, William W. Seeley, Michal A. Surma, Christian Klose, Joao A. Paulo, Andrew D. Nguyen, J. Wade Harper, Tobias C. Walther, Robert V. Farese Jr. bioRxiv 2021.09.30.461806; doi: https://doi.org/10.1101/2021.09.30.461806
ensemblQueryR
By onA package allowing easy integration of Ensembl querying with a user’s R workflow.
