Lentivirus plasmid: pLV[Exp]-U6>KAT8_P1_Seq1-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.
Isolation of NeuN+ cells from brain tissue (for CUT and RUN)
By savannah onThis protocol describes the steps to isolate NeuN+ cells from brain tissue in preparation for CUT and RUN.
Lentivirus plasmid: pLV[Exp]-U6>KAT8_P1_Seq1-hPGK>mApple
By savannah onPlasmid vector encoding a sgRNA sequence which targets the human KAT8 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV backbone.
Single cell/nuclei RNAseq analysis
By savannah onThis 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.
Lentivirus plasmid: pLV[Exp]-U6>KANSL1_P1_Seq1-hPGK>mApple
By savannah onPlasmid vector encoding a sgRNA sequence which targets the KANSL1 promoter from CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV backbone.
Generation of human-induced pluripotent-stem-cell-derived cortical neurons for high-throughput imaging of neurite morphology and neuron maturation
By savannah onA STAR protocol that describes how to differentiate cryopreserved human cortical neuronal progenitors into mature cortical neurons for high-throughput imaging analysis.
KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy
By savannah onPublished: The KAT8 gene encodes a lysine acetyltransferase and represents the catalytically active subunit of the non-specific lethal (NSL) epigenetic remodeling complex. The authors’ study provided additional support for KAT8 inhibition as a regulator of mitophagy and autophagy processes. View original preprint.
A mono- and intralink filter (mi-filter) to reduce false identifications in cross-linking mass spectrometry data
By savannah onThe authors show that this simple and intuitive filter has a dramatic effect on different types of cross-linking data ranging from individual protein complexes over medium-complexity affinity enrichments to proteome-wide cell lysates and significantly reduces the number of false-positive identifications for inter-protein links in all these types of XL-MS data.
Image processing of full-length monomeric LRRK2
By savannah onThis 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.
ensemblQueryR
By savannah onA package allowing easy integration of Ensembl querying with a user’s R workflow.
LRRK1 expression and purification
By savannah onProtein purification protocol for full-length LRRK1 as done by Leschziner and Reck-Peterson Labs. Original protocol by Janice M. Reimer and Yu Xuan Lin.
Quick guide to use paceTOMO for cryo-ET data collection from Titan Krios
By savannah onThis 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.
Alpha-synuclein immunochemistry on STC-1 cells using DAB
By savannah onThis 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).
Constructs and generation of stable cell lines
By savannah onProtocol 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.
Differential response of α-synuclein expression to bacterial ligands and metabolites in mouse enteroendocrine cells
By savannah onDataset for manuscript, "α-synuclein expression in response to bacterial ligands and metabolites in gut enteroendocrine cells." Tabs in excel file are titled with the figure number.
Differentiation NPCs to dopaminergic/midbrain neuron
By savannah onThis 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).
Endogenous coimmunoprecipitation
By savannah onProtocol used for immunoprecipitation of HSP60 and LONP1 in HEK cells to show the interaction with V5-Flag-tagged WT-GCase.
Expansion microscopy
By savannah onExpansion microscopy is a technique to visualize biological structures with higher spatial resolution than traditional microscopy methods.
Flag co-immunoprecipitation
By savannah onProtocol used to pull down V5-FLAG-Gcase interacting proteins in HEK cells.
GCase co-immunoprecipitation
By savannah onThe authors developed this protocol to identify protein-protein interactions between the enzyme glucocerebrosidase (GCase) and other proteins in human iPSC-derived Neural Precursor Cells.
