Hydrop enables droplet-based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads
By onThe data available in this repository can be used to replicate all the figures in the authors’ manuscript using their data analysis tutorial available at https://github.com/aertslab/hydrop_data_analysis.
APEX-ATG8 proteomics with and without lysosomal damage
By onProteomics data associated with DOI: 10.7554/eLife.72328
Thawing of hPSCs grown on MEFs
By onThis protocol describes the standard procedure of thawing human pluripotent stem cells (hPSCs) on inactivated mouse embryonic fibroblasts (MEFs).
pGBdest-10xHis-TEV-ATG5_ATG7_ATG10_ATG12_ATG16L1_F32A-I35A-I36A_-GFP-TEV-StrepII
By onPlasmid: Plasmid for the Expression of the E3 complex with an FII (F32A, I35A, and I36A) mutation. SMC Internal reference: SMC1728
Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain
By onCrossing the blood–brain barrier in primates is a major obstacle for gene delivery to the brain. Adeno-associated viruses (AAVs) promise robust, non-invasive gene delivery from the bloodstream to the brain. However, unlike in rodents, few neurotropic AAVs efficiently cross the blood–brain barrier in non-human primates. Here we report on AAV.CAP-Mac, an engineered variant identified by screening in adult marmosets and newborn macaques, which has improved delivery efficiency in the brains of multiple non-human primate species: marmoset, rhesus macaque and green monkey. CAP-Mac is neuron biased in infant Old World primates, exhibits broad tropism in adult rhesus macaques and is vasculature biased in adult marmosets. We demonstrate applications of a single, intravenous dose of CAP-Mac to deliver functional GCaMP for ex vivo calcium imaging across multiple brain areas, or a cocktail of fluorescent reporters for Brainbow-like labelling throughout the macaque brain, circumventing the need for germline manipulations in Old World primates. As such, CAP-Mac is shown to have potential for non-invasive systemic gene transfer in the brains of non-human primates.
H9 ES AAVS1-NGN2 FAM134C/A/B-/-;TEX264-/-; PiggyBac-Keima-RAMP4
By onES cells were modified to create iNeurons lacking ER-phagy receptors FAM134C, A, B, TEX264, and expressing Keima-RAMP4 ER-phagy flux reporter. CRISPR/Cas9 was used to introduce NEUROG2 construct in AAVS1 locus and knockout RETREG and TEX264 genes.
pCAG- WIPI2dK88E-cs- TEV-STREP
By onPlasmid: Mammalian expression of human WIPI2d K88E with C-terminal Strep.
ALS and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy
By onSource data for manuscript https://doi.org/10.5281/zenodo.4670341
Proteostasis and lysosomal quality control deficits in Alzheimer’s disease neurons
By onLysosomal quality control (LQC) pathways are notably impaired in both aging and AD, leading to neuronal vulnerability and cytotoxicity. Neurons show amyloid-β inclusions, and enhancing lysosomal function can help alleviate AD-related pathologies.
3D FIBSEM CLEM
By onThis protocol details the procedure of Correlative Light Microscopy and Electron Microscopy (CLEM) with 3D Focus Ion Beam Scanning Electron Microscopy (FIBSEM) technique in Zeiss Crossbeam 550 FIBSEM system.
Structure of human ULK1C:PI3KC3-C1 supercomplex
By onStructure of human ULK1C:PI3KC3-C1 supercomplex
pCAG-MBP-Foldon-ATG9 (801-839)
By onPlasmid: To make ATG9 C-terminal tail trimer for expression in mammalian cells.
Differential response of α-synuclein expression to bacterial ligands and metabolites in mouse enteroendocrine cells
By onDataset for manuscript " α-synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells". Tabs in excel file are title with the figure number.
Structural and biochemical insights into lipid transport by VPS13 proteins
By onVPS13 proteins are proposed to function at contact sites between organelles as bridges for lipids to move directionally and in bulk between organellar membranes. VPS13s are anchored between membranes via interactions with receptors, including both peripheral and integral membrane proteins. Here we present the crystal structure of VPS13s adaptor binding domain (VAB) complexed with a Pro-X-Pro peptide recognition motif present in one such receptor, the integral membrane protein Mcp1p, and show biochemically that other Pro-X-Pro motifs bind the VAB in the same site. We further demonstrate that Mcp1p and another integral membrane protein that interacts directly with human VPS13A, XK, are scramblases. This finding supports an emerging paradigm of a partnership between bulk lipid transport proteins and scramblases. Scramblases can re-equilibrate lipids between membrane leaflets as lipids are removed from or inserted into the cytosolic leaflet of donor and acceptor organelles, respectively, in the course of protein-mediated transport.
Transfection and protein over-expression
By onThis protocol provides the details for how to transfect and harvest 3X-FLAG-SHIP164Δ901-1099
APEX-Galectin proteomics with and without lysosomal damage
By onProteomics data associated with DOI: 10.7554/eLife.72328
Genome-wide determinants of mortality and clinical progression in Parkinson’s disease – Summary statistics
By onSummary statistics from "Genome-wide determinants of mortality and clinical progression in Parkinson’s disease."
TBK1 knockdown and rescue in Hela-M cells
By onThis protocol transiently depletes TBK1 from HeLa cells and re-introduces a tagged TBK1 along with other relevant components of mitophagy.
