Protocol Archive

Single-cell dissociation of brain organoids

This protocol details the steps for DNA extraction from a human blood sample, quality control, and SNP and APOE genotyping. The protocol has been adapted from the PRoBaND SNP Genotyping and ApoE Genotyping Protocol

Method that allows the staining of intact Golgi using GolgiTracker for subsequent flow cytometry analysis. The analysis can provide a quantitative indication of the level of enrichment of the organelle immunoprecipitationand can be used as a quality control check for the purity of the immunoprecipitated Golgi.

This Standard Operating Procedure (SOP) describes the safe use of vibratomes.

This protocol describes the statistical analysis applied to the quantifications in Chang et al. 2021 SA paper.

Protocol for striatal dopamine measurement in mouse brain

This protocol describes the procedure of subtomogram averaging and 3D classification of VPS13C rod-shaped densities inside cryotomograms of mammalian cells. Sub-tomogram averaging package i3 was used for 3D alignment and classification.

This protocol details Surface Density Calculation.

This protocol describes surface protein labeling with biotin using EZ-Link Sulfo-NHSLC-Biotin. This chemical reacts with primary amines such as lysine but does not permeate cell membranes because of the charge. Thus, it only biotinylates surface proteins.

This protocol details Tube Radius Calculation.

This protocol details methods for the unilateral intranigral AAV alpha-synuclein injection.

This protocol describes the immunoblotting for components of the LRRK2 signalling pathway (LRRK2, LRRK2 pS935 and phospho-Rabs) using Invitrogen NuPage SDS-PAGE reagents and the BioRad Turbo Blot transfer system.

WIPI2d cloning.

Pulldown assay of WIPI2d.

WIPI2d expression and purification from HEK cells.

Protocol for sample preparation and live fluorescence imaging of yeast cells.

This protocol details the procedure to assess mitophagy by analyzing COXII degradation via Western blotting.

This is a collection of protocols used in a recent pre-print by the Deleidi Lab, Team Schapira. You can access pre-print at https://doi.org/10.21203/rs.3.rs-1521848/v1

Lyso-IP is a method that allows for the isolation of lysosomes for proteomics and metabolomics (dx.doi.org/10.17504/protocols.io.bybjpskn; dx.doi.org/10.17504/protocols.io.bx9hpr36). We have developed an analogous approach for purification of early/sorting endosomes (Endo-IP).

This protocol describes how to plunge-freeze yeast on EM grids and how to target autophagic structures by combining cryo confocal fluorescence data to FIB-milling and tomogram acquisition.