FM1-43 endocytic uptake assay in HIPSC derived neurons
By onFM1-43 is a lipophilic styryl dye, nontoxic to the cells, virtually nonfluorescent in aqueous media. The dye will become fluorescent once it binds to the plasma membrane. In neurons that are actively releasing neurotransmitters, these dyes become internalized within the recycled synaptic vesicles, and the nerve terminals become brightly stained. This shows an increase in the fluorescence intensity of FM1-43. When the cells undergo another stimulation (through KCL or electrical) the FM1-43 dye containing vesicles will be released through exocytosis. Thus, resulting in a decrease in the FM1-43 fluorescence intensity.
pCAG-OSF-ATG13 (2-197)
By onPlasmid: To make ATG101/ATG13 HORMA complex for expression in mammalian cells.
Rotarod Test to assess motor coordination in a mouse parkinsonian model
By onThis protocol evaluates motor coordination in the rotarod assay in parkinsonian mice.
Flag co-immunoprecipitation
By onProtocol used to pull down V5-FLAG-Gcase interacting proteins in HEK cells
Freezing of hPSCs grown on MEFs
By onThis protocol describes the standard procedure of freezing human pluripotent stem cells (hPSCs), which were grown on inactivated mouse embryonic fibroblasts (MEFs).
Cryo-ET of S. cerevisiae during starvation (tomograms)
By onCryo-ET of S. cerevisiae during starvation (tomograms).
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By onR package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Lipid transfer assay
By onThis protocol details how to perform a lipid transfer assay with 3xFLAG-SHIP164Δ901-1099
H9 ES AAVS1-NGN2 CCPG1-/-
By onES cells modified using CRISPR/Cas9 lack the ER-phagy receptor CCPG1. NEUROG2 gene was introduced using a TRE3G promoter in AAVS1 locus. The cells are human embryonic stem cells derived from blastocysts.
pCAG-OSF-ATG13 (2-197)-E83L
By onPlasmid for expression of human ATG13 HORMA E83L mutant in mammalian cells
HEK293T FBXO7-/-
By onHEK293T cells were genetically modified using CRISPR/Cas9 to delete the FBXO7/PARK15 gene.
Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease
By onAuxilin participates in clathrin uncoating to facilitate presynaptic endocytosis. Loss-of-function mutations of auxilin (PARK19) cause Parkinson’s disease. Using auxilin KO mice, Vidyadhara et al. (2023) show that synaptic vesicle sorting deficits, cytoplasmic dopamine accumulation, dopamine transporter mistrafficking, and synaptic autophagic overload may lead to pathogenesis of Parkinson’s disease in PARK19 patients. This file contains the data set used to generate all the main figures.
Custom open-chamber microfluidic fabrication
By onThis protocol described the fabrication of two- and three-open chambered microfluidics suitable for cell culturing using commercially acquired master mould.
H9 ES AAVS1-NGN2 FAM134C/A-/-; PiggyBac-Keima-REEP5
By onES cells were modified using CRISPR/Cas9 to express NEUROG2 and Keima-REEP5 for ER-phagy studies. Knockouts RETREG2 and RETREG3 were created, and cells were derived from a blastocyst stage female human embryonic stem cell line.
Proteomics workflow for whole cell lysate, endosome, and lysosome fractions
By onA protocol for sample preparation for LC-MS analysis of whole cell lysates and for lysosomal and endosomal fractions purified by Lyso-IP and Endo-IP.
Cell-based Tau seeding assay
By onProtocol outlines Tau seeding techniques in cellular model for research purposes.
Membrane interaction and mechanism of LC3 lipidation machinery in autophagy – Raw GUV data
By onRaw GUV data of fluorescent protein imaged on a Nikon A1 confocal microscope with a 63 × Plan Apochromat 1.4 NA objective. Three biological replicates were performed for each experimental condition. Identical laser power and gain settings used.
A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data
By onSingle-cell RNA-sequencing technology enables the identification of cell-type-specific differential gene expressions. MARBLES, a new statistical model, effectively detects DE genes across conditions.
