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  • RNA extraction and quantitative PCR to assay inflammatory gene expression

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    Protocol for RT-qPCR to test levels of NF-kB response genes in a cell model transiently over-expressing Parkin. We found upregulation of key pro-inflammatory genes normalized to housekeeping gene, Gapdh.

  • Open Field Test to assess motor coordination in a mouse parkinsonian model

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    The 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

  • powerEQTL: An R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis

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    Genome-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.

  • pCAG-mcherry- WIPI2dC93E-cs- TEV -STREP

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    Plasmid for mammalian expression of human WIPI2d C93E with N-terminal mCherry and C-terminal Strep.

  • His-ATG3-Y209A

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    Plasmid for ATG3 mutant Y209A overexpression in E.Coli.

  • Coating coverslips for cell culture

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    Coated coverslips provide a nourishing adherent surface for cell culture. This protocol provides step by step instruction on how to coat coverslips for cell culture.

  • Code for extraction of any user-defined information from uniprot

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    Code for extraction of any user-defined information from Uniprot.

  • Sample vitrification and cryo-EM data acquisition

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    Protocol describing sample vitrification and cryo-EM data acquisition.

  • Fixing hippo neurons to assess endogenous NEMO during oxidative stress

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    Protocol describing the procedure for fixing Hippocampal rat neurons to assess endogenous NEMO during oxidative stress.

  • GFP-WIPI2d-TEVcs-TSF

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    Plasmid: For the purification of GFP- WIPI2d protein.

  • TMT proteomic data from mouse cortical neurons

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    TMT proteomic data from mouse cortical neurons

  • Cell culture, transfection, immunocytochemistry, and imaging

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    This protocol is to help with the maintenance, transfection, immunocytochemistry, and imaging of adherent mammalian cells

  • immunofluorescent staining with anti-GFP and anti-CD63 antibodies

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    immunofluorescent staining with anti-GFP and anti-CD63 antibodies

  • AAVS1-SA-neo-CAGGS-PE2-2A-GFP

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    It can be used to generate knock-in cell line faciliating prime editing. 

  • Subcellular proteomics of dopamine neurons in the mouse brain

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    Understanding the proteome of dopamine neuron is difficult due to the complex cytoarchitecture of the neurons. The authors were able to map the somatodendritic and axonal proteomes of midbrain dopaminergic neurons.

  • Free-floating Mouse Brain Immunohistochemistry

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    This protocol enables immunohistochemical staining of murine tissue with superior penetration of the tissue by the reagents due to the free-floating approach.

  • Expansion of mouse embryonic fibroblasts (MEFs) for hPSC cultures

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    This protocol describes the expansion of mouse embryonic fibroblasts (MEFs) as feeder cells for human pluripotent stem cell (hPSC) culture.

  • Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures

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    Recent 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

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    Variants 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.

  • Genetic and pharmacological reduction of CDK14 mitigates synucleinopathy

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    Decreasing alpha-synuclein levels is a potential therapeutic approach for synucleinopathies. The authors identified CDK14 regulates alpha-synuclein and show reduction of CDK14 reduces alpha-synuclein and PD-like characteristics.

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