HyDrop-RNA v1.0
By Michelle onStep-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
powereQTL – An R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By taliag onAn R shiny application for calculating sample size and power of bulk tissue and single-cell eQTL analysis
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy
By Blythe Lloyd onPublished: Selective 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. They found that the core machinery engaged during mitophagy depends on different autophagy receptors, but LC3 lipidation is a universal feature. View original preprint.
Microfluidic Chip Production v1.1 V.2
By Michelle onProtocol for producing microfluidic chips used in HyDrop experiment.
ALS- and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy
By Blythe Lloyd onPublished: TBK1 mutations are linked to neurodegenerative disorders. The authors explored how TBK1 functions in PINK1/Parkin-dependent mitophagy and how mutations lead to disease. TBK1 recruitment and kinase activity contributed to the clearance of damaged mitochondria (mitophagy). Further, they showed that TBK1 presence alone could disrupt the mitochondrial network. View original preprint.
Chemically induced senescence in human stem cell‐derived neurons promotes phenotypic presentation of neurodegeneration
By taliag onPublished: Using embryonic stem-cell derived neurons to model age-related neurodegenerative diseases is inherently difficult. The authors thereby developed a chemical cocktail to induce cellular senescence (without causing DNA damage), thereby inducing embryonic cells to exhibit features characteristic of aged cells. The cocktail can help enhance disease-related phenotypes in iPSCs.
Glucocerebrosidase 1 and leucine-rich repeat kinase 2 in Parkinson disease and interplay between the two genes
By Michelle onReview: This review focuses on the endolysosomal pathway roles of GBA and LRRK2, highlighting the role and activity of Rab GTPases as LRRK2 substrates.
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
By taliag onPublished: Genome-wide association studies (GWAS) reveal thousands of genetic loci. To understand the causality of the genetic variants, many researchers employ expression of quantitative trait locus (eQTL) analysis. The authors created a simplified, user-friendly R package called powerEQTL to aid in performing the power calculations needed for eQTL analysis. View original preprint.
Raw tomogram of GFP-a-synuclein inclusion in primary mouse neuron expressing GFP-a-synuclein, seeded with PFFs
By Blythe Lloyd onRaw data associated with DOI: 10.1038/s41467-021-22108-0
Raw tomogram of endogenous a-synuclein inclusion in primary mouse neurons seeded with PFFs
By Blythe Lloyd onRaw data associated with DOI: 10.1038/s41467-021-22108-0
fcs files to “The extracellular chaperone Clusterin enhances Tau aggregate seeding in a cellular model”
By Blythe Lloyd onDataset associated with DOI: 10.17617/3.51VXU0
The remote assessment of parkinsonism supporting the ongoing development of interventions in Gaucher disease
By taliag onPublished: This methodology report assesses a large cohort of GBA mutation carriers with the goal of developing procedures to diagnose PD earlier. View original preprint.
APEX-ATG8 proteomics with and without lysosomal damage
By Blythe Lloyd onProteomics data associated with DOI: 10.7554/eLife.72328
APEX-Galectin proteomics with and without lysosomal damage
By Blythe Lloyd onProteomics data associated with DOI: 10.7554/eLife.72328
Protocol for hippocampal neuronal cultures
By Blythe Lloyd onThis protocol details the procedure for preparation of neuronal cultures from mice hippocampi as it was performed in https://doi.org/10.1083/jcb.202010004 but can also be used to prepare cultures of cortical neurons.
APEX-autophagy cargo receptor proteomics with and without lysosomal damage
By Blythe Lloyd onProteomics data associated with DOI: 10.7554/eLife.72328