Protocol Archive

Associated with preprint: https://doi.org/10.1101/2023.06.26.546565

Associated with preprint: https://doi.org/10.1101/2023.06.26.546565

Associated with preprint: https://doi.org/10.1101/2023.06.26.546565

This protocol describes the preparation and culture of mouse primary cortical neurons for live-imaging experiments. Neurons were transfected 16-24 hours before imaging using Lipofectamine 2000.

The authors developed this protocol to test levels of NF-kB response genes in a cell model transiently over-expressing Parkin. With this technique the authors found significant upregulation of key pro-inflammatory genes normalized to a housekeeping gene, Gapdh.

This protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.

The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots.

This protocol describes the steps to isolate NeuN+ cells from brain tissue in preparation for CUT and RUN.

This protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript, "L1retrotransposons drive human neuronal transcriptome complexity and functional diversification," from fetal forebrain and adult prefrontal cortex tissue.

This protocol assumes that 2000 to 4000 movies of full-length LRRK2 embedded on vitreous ice are collected with an electron microscope equipped with a direct detector. It focuses primarily on the monomeric population of LRRK2 and has been leading to 3-4 Å resolution structures.

Protein purification protocol for full-length LRRK1 as done by Leschziner and Reck-Peterson Labs. Original protocol by Janice M. Reimer and Yu Xuan Lin.

This quick guide provides key minimal steps for preparing the Titan/SerialEM for the tomogram data collection on lamella or in vitro specimens with a K3 camera. paceTOMO routine is also included for a typical tomogram data collection session. Please note that this is not an exhaustive guide, but summarizes the order of key steps.

This protocol describes how to visualize alpha-synuclein in STC-1 cells by DAB immunohistochemistry. It also works for other antibodies (e.g., 5-HT, CCK, GLP).

Protocol used to generate stable Flp-In T-REx-HEK 293 cell lines expressing WT or mutant GCase (E326K or L444P) as a V5-FLAG-tagged protein using a tetracycline-inducible system.

This protocol is part of a collection of protocols (dx.doi.org/10.17504/protocols.io.8epv593dng1b/v1) for the paper, "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" (https://doi.org/10.21203/rs.3.rs-1521848/v1).

Protocol used for immunoprecipitation of HSP60 and LONP1 in HEK cells to show the interaction with V5-Flag-tagged WT-GCase.

Expansion microscopy is a technique to visualize biological structures with higher spatial resolution than traditional microscopy methods.

Protocol used to pull down V5-FLAG-Gcase interacting proteins in HEK cells.

The authors developed this protocol to identify protein-protein interactions between the enzyme glucocerebrosidase (GCase) and other proteins in human iPSC-derived Neural Precursor Cells.

iPSC generation and gene correction (CRISPR-CAS9) protocol.