Generation of induced pluripotent stem cells and gene correction
By savannah oniPSC generation and gene correction (CRISPR-CAS9) protocol.
Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism – ASAP protocol collection
By savannah onCollection of protocols of Deleidi Lab used in the publication: "Glucocerebrosidase is imported into mitochondria and preserves complex I integrity and energy metabolism."
Immunofluorescence staining
By savannah onThis protocol describes the immunofluorescence staining of cells.
Immunohistochemistry using paraffin embedded tissue
By savannah onThe protocol works for many other antibodies and the only change necessary for most antibodies is determining the optimal dilution of the primary antibody and the best type of antigen-retrieval to use.
Indirect Proximity Ligation Assay (PLA) – Brightfield
By savannah onThe authors describe the PLA protocol that is routinely used in the laboratory to detect nitrated alpha-synuclein and nitration of mitochondrial enzymes such as SOD2 and the mitochondrial complex 1 subunit NDUFB8.
Live-cell imaging
By savannah onLive-cell imaging is a technique to visualize dynamic cellular processes in living biological samples.
Measurement of GLP-1 release in cell supernatant from Hutu-80 enteroendocrine cells via ELISA
By savannah onThis was adapted from Cat. # EGLP-35K to optimize the seeding density of the assay based on the cell line used (Hutu 80 enteroendocrine cells RRID: CVCL_1301); moreover, cell line used and media conditions used to characterize GLP-1release. The lowest level of GLP-1 that can be detected by this assay is 2 pM (100ul plasma sample size).
Mito and glycolysis stress tests for enteroendocrine cells – Hutu-80
By savannah onComparing two cultures of a similar passage number, cell density, time that the cells have been in culture, and time since the medium was changed as all this influences mitochondrial respiration has proven best. Culture cells until they are almost/just confluent. Cell should have been fed recently before use.
Mitochondrial complex activity assays
By savannah onMitochondria complex activity assays measure the activity levels of the different complexes of the mitochondrial electron transport chain (ETC).
Neuromelanin staining (Fontana-Masson staining)+ TH-DAB staining on midbrain organoids
By savannah onThe authors combined it with DAB-TH staining that works by using an antibody to detect the presence of TH, followed by a reaction with a substrate (DAB) that results in the formation of a brown-colored product at the site of the antigen-antibody interaction.
Phenotypic effect of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study
By savannah onPublished: The authors’ results support previous evidence that GBA1-positive PD has a specific phenotype with more severe non-motor symptoms. However, the authors did not reproduce previous findings of more frequent prodromal PD signs in non-affected GBA1 carriers. View original preprint.
Plasmid-reprogramming of human fibroblasts
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).
qPCR of α-synuclein, TNF, and NF-κβ
By savannah onA procedure for quantitative real time reverse transcription PCR of α-synuclein, TNF, and NF-κβ.
R code for paper Phenotype of GBA1 variants in individuals with and without Parkinson’s disease: The RAPSODI study
By savannah onThis is the R code used to produce the results described in the paper.
R Code used in “Sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease”
By savannah onR Code used in "sex-specific microglial responses to glucocerebrosidase inhibition: Relevance to GBA1-linked Parkinson’s disease."
Sex-specific microglial responses to glucocerebrosidase inhibition
By savannah onMorpho-dynamic analysis occurring in primary cells derived from female and male mice in response to proinflammatory stimulations and glucocerebrosidase inhibition.
Soluble and insoluble A-SYN fractionation
By savannah onSoluble/insoluble alpha-synuclein fractionation is a technique used to separate different forms of the alpha-synuclein protein based on their solubility properties.
Dopamine transporter and synaptic vesicle sorting defects underlie auxilin-associated Parkinson’s disease
By savannah onAuxilin participates in clathrin uncoating to facilitate presynaptic endocytosis. This file contains the data set used to generate all the main figures of loss-of-function mutations of auxilin (PARK19 using KO mice, Vidyadhara et al., 2023 to show that synaptic vesicle sorting deficits, cytoplasmic dopamine accumulation, dopamine transporter mistrafficking, and synaptic autophagic.
Fecal metagenomic sequencing data for PD patients and controls from Rush University Medical Center
By savannah onFecal metagenomic sequencing data associated with Boktor et al. (2023). This dataset includes samples from the Rush University Medical Center cohort.
