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.
A computational pipeline to quantify primary cilia in mouse embryonic fibroblasts with CellProfiler
By savannah onThis protocol works with .czi format images which are acquired using a Zeiss laser scanning confocal microscope and are maximum intensity projected.
Preparation of unilamellar liposomes
By savannah onThe authors present here a protocol for preparing liposomes that can be used to monitor binding of proteins to vesicles of various membrane curvatures. The authors used this to study the association of the PPM1H phosphatase with highly curved membranes due to its N-terminal amphipathic helix.
Gibson Assembly Cloning
By savannah onGibson assembly requires a vector backbone and one or more inserts that have been PCR amplified. The inserts should have 15-20 base pairs of overlap at ligation sites, so primers used to amplify the inserts should contain a tail overhang with this homology. The vector backbone should be linear.
Lentivirus plasmid: pLV[Exp]-U6>PINK1_P1_Seq3-hPGK>mApple
By savannah onPlasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV backbone.
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.
Macros and pipelines for analysis of image analysis
By savannah onImageJ macros and pipelines for analysis of pUb puncta, Keima Ratio, p62nuclei, and Parkin recruitment to mitochondria.
Proteomics of iNeurons or HeLa cells with or without FBXO7
By savannah onTMT proteomics datasets from FBXO7-/- hESC differentiation to iNeurons and HeLa cells.
Proteostasis and lysosomal quality control deficits in Alzheimer’s disease neurons
By savannah onCompounds enhancing lysosomal function broadly ameliorate AD-associated pathologies. The authors’ findings establish cell-autonomous LQC dysfunction in neurons as a central vulnerability in aging and AD pathogenesis.
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
Scripts for analysis of total proteomes in response to nutrient stress
By savannah onScripts for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Web portal (shiney ap) for analysis of total proteomes in response to nutrient stress
By savannah onWeb portal (shiney app) for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Astrocyte isolation and culturing
By savannah onThis protocol details steps for preparing an astrocyte monoculture from mouse pups. From dissection to plated samples ready to be transfected, treated, lysed, or imaged, the protocol takes 20-25 days.
Cell lysis and gel electrophoresis for protein analysis of HeLa cells
By savannah onThe authors present multiple protocols used for biochemical analysis of protein expression and association. The authors’ studies demonstrated that NEMO recruitment to damaged mitochondria occurs in specific circumstances, and NEMO colocalization with p62 is also dependent on multiple factors.
Co-immunoprecipitation using GFP-trap
By savannah onThe authors describe performing co-immunoprecipitation experiments in HEK293 cells using GFP-trap beads.
