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.
Expansion of mouse embryonic fibroblasts (MEFs) for hPSC cultures
By onThis protocol describes the expansion of mouse embryonic fibroblasts (MEFs) as feeder cells for human pluripotent stem cell (hPSC) culture.
AAVS1-SA-neo-CAGGS-PE2-2A-GFP
By onIt can be used to generate knock-in cell line faciliating prime editing.
Subcellular proteomics of dopamine neurons in the mouse brain
By onUnderstanding 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.
Cell culture, transfection, immunocytochemistry, and imaging
By onThis protocol is to help with the maintenance, transfection, immunocytochemistry, and imaging of adherent mammalian cells
Macros and pipelines for analysis of image analysis
By onImageJ macros and pipelines for analysis of pUb puncta, Keima Ratio, p62nuclei and Parkin recruitment to mitochondria.
Basal ganglia neurons in healthy and parkinsonian primates generate recurring sequences of spikes
By onBasal ganglia neurons fire in recognizable, repeating sequences of interspike intervals (ISIs), the incidence of which is influenced by the induction of Parkinsonism.
Rodent models based on endolysosomal genes involved in PArkinson’s disease
By onGenes linked to endolysosomal function are connected to Parkinson's disease, suggesting a role in its development. Rodent models targeting these genes like LRRK2 and GBA1 show parkinsonian features, aiding in understanding and treating the disease.
Genetic and pharmacological reduction of CDK14 mitigates synucleinopathy
By onDecreasing 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.
