Open Field Test to assess motor coordination in a mouse parkinsonian model
By onThe Open Field task is a simple sensorimotor test used to determine general activity levels, gross locomotor activity, and exploration habits in rodent models of CNS disorders. Open Field Test
Detection of Tau ubiquitylation
By onThis protocol is associated with the following preprint, published on February 19th 2022: The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds Itika Saha, Patricia Yuste-Checa, Miguel Da Silva Padilha, Qiang Guo, Roman Körner, Hauke Holthusen, Victoria A. Trinkaus, Irina Dudanova, Rubén Fernández-Busnadiego, Wolfgang Baumeister, David W. Sanders, Saurabh Gautam, Marc I. Diamond, F. Ulrich Hartl, Mark S. Hipp bioRxiv 2022.02.18.481043; doi: https://doi.org/10.1101/2022.02.18.481043
Rapalog-induced chemical dimerization experiments
By onThis protocol describes how to conduct Rapalog-induced chemical dimerization experiments.
cDNA clones for expression of MitoTag (OMP25) in mammalian cells
By onPlasmids for expression of OMP25 (MitoTag) in human and mouse cells.
Bulk NGS/allele quantification – Highly efficient generation of isogenic pluripotent stem cell models using prime editing
By onThis file contains sequencing results for amplicons covering specific regions of interest related to prime editing of hPSCs
pCAG-MBP-Foldon-ATG9 (830-839)
By onPlasmid: To make ATG9 C-terminal tail trimer for expression in mammalian cells.
immunofluorescent staining with anti-GFP and anti-CD63 antibodies
By onimmunofluorescent staining with anti-GFP and anti-CD63 antibodies
Fixing hippo neurons to assess endogenous NEMO during oxidative stress
By onProtocol describing the procedure for fixing Hippocampal rat neurons to assess endogenous NEMO during oxidative stress.
Code for extraction of any user-defined information from uniprot
By onCode for extraction of any user-defined information from Uniprot.
Sample vitrification and cryo-EM data acquisition
By onProtocol describing sample vitrification and cryo-EM data acquisition.
Coating coverslips for cell culture
By onCoated coverslips provide a nourishing adherent surface for cell culture. This protocol provides step by step instruction on how to coat coverslips for cell culture.
powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
By onGenome-wide association studies (GWAS) have revealed thousands of genetic loci for common diseases. One of the main challenges in the post-GWAS era is to understand the causality of the genetic variants. Expression quantitative trait locus (eQTL) analysis has been proven to be an effective way to address this question by examining the relationship between gene expression and genetic variation in a sufficiently powered cohort. However, it is often tricky to determine the sample size at which a variant with a specific allele frequency will be detected to associate with gene expression with sufficient power. This is particularly demanding with single-cell RNAseq studies. Therefore, a user-friendly tool to perform power analysis for eQTL at both bulk tissue and single-cell level will be critical. Here, we presented an R package called powerEQTL with flexible functions to calculate power, minimal sample size, or detectable minor allele frequency in both bulk tissue and single-cell eQTL analysis. A user-friendly, program-free web application is also provided, allowing customers to calculate and visualize the parameters interactively.
twichma/Sequence-and-pattern-detection: Sequence and pattern detection code
By onThe code provided is for analyzing sequences and patterns.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures
By onRecent findings identified PD-associated autoimmune features. Using RNA sequencing, the authors found a broad gene expression profile in memory T cells and a specific PD-associated gene signature.
Genetic variations in GBA1 and LRRK2 genes: Biochemical and clinical consequences in Parkinson disease
By onVariants in the GBA1 and LRRK2 genes are the most common genetic risk factors associated with Parkinson disease (PD). Both genes are associated with lysosomal and autophagic pathways, with the GBA1 gene encoding for the lysosomal enzyme, glucocerebrosidase (GCase) and the LRRK2 gene encoding for the leucine-rich repeat kinase 2 enzyme. GBA1-associated PD is characterized by earlier age at onset and more severe non-motor symptoms compared to sporadic PD. Mutations in the GBA1 gene can be stratified into severe, mild and risk variants depending on the clinical presentation of disease. Both a loss- and gain- of function hypothesis has been proposed for GBA1 variants and the functional consequences associated with each variant is often linked to mutation severity. On the other hand, LRRK2-associated PD is similar to sporadic PD, but with a more benign disease course. Mutations in the LRRK2 gene occur in several structural domains and affect phosphorylation of GTPases. Biochemical studies suggest a possible convergence of GBA1 and LRRK2 pathways, with double mutant carriers showing a milder phenotype compared to GBA1-associated PD. This review compares GBA1 and LRRK2-associated PD, and highlights possible genotype-phenotype associations for GBA1 and LRRK2 separately, based on biochemical consequences of single variants.
Free-floating Mouse Brain Immunohistochemistry
By onThis protocol enables immunohistochemical staining of murine tissue with superior penetration of the tissue by the reagents due to the free-floating approach.
