H9 ES AAVS1-NGN2 FAM134C-/-; PiggyBac-Keima-RAMP4
By onES cells were modified using CRISPR/Cas9 to lack FAM134C and express Keima-RAMP4 ER-phagy flux reporter. NEUROG2 construct was introduced in AAVS1 safe harbor locus. Cells are embryonic stem cells derived from a female human at blastocyst stage.
Crystallization, data collection and structure solution of PxP-VAB
By onProtocol lists the steps to obtain PxP(Mcp1ct)-VABct crystals, X-ray diffraction data acquisition and obtaining the structure solution using molecular replacement with a model generated by AlphaFold2.
Scripts for analysis of total proteomes in response to nutrient stress
By onScripts for analysis of total proteomes in response to nutrient stress. Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Mito-Keima assay to assess mitophagy
By onThis protocol details the procedure of mito-Keima assay to assess mitophagy.
pCAG-OSF-ATG13 (2-197)-F19D
By onPlasmid: Expresses human ATG13 HORMA F19D mutant in mammalian cells.
Single-cell Whole Genome Amplification (scWGA) of human post-mortem brain samples isolated by Laser Capture Microdissection (LCM)
By onThis protocol uses Laser Capture Microdissection (LCM) technology on human post-mortem brain tissue slides in order to do low coverage single-cell whole genome sequencing to detect mega-base somatic Copy Number Variations (CNVs).
Tail suspension test to assess depression/anxiety behavior in parkinsonian mice
By onThe Tail Suspension Test is a mouse behavioral paradigm measuring behavioral despair or “depression-like” behavior and learned helplessness.
Inhibition of striatal dopamine release by the L-type calcium channel inhibitor isradipine co-varies with risk factors for Parkinson’s
By onThis data show that LTCC function in DA axons, and isradipine effect, are locally governed and suggest they vary in a manner that in turn might impact on, or reflect, the cellular stress that leads to parkinsonian degeneration.
Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3-YIPF4 as membrane receptors for Golgiphagy
By onMacroautophagy degrades cellular macromolecules during nutrient stress, providing building blocks and remodeling the proteome. YIPF3 and YIPF4 are identified as receptors for Golgiphagy, crucial for eliminating Golgi membrane proteins.
Metagenomics of Parkinson’s disease implicates the gut microbiome in multiple disease mechanisms
By onA study on Parkinson's disease links gut microbiome to brain health. Analysis of 490 PD patients and 234 controls reveals dysbiosis, microbial clusters, and disease-promoting factors in PD microbiome, offering insights for future research.
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308
By onPython script used to generate the heatmap representation of identified high-confident LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308.
Immunofluorescence assay (IFA)
By onThis protocol details the procedure of immunofluorescence assay (IFA).
Differentiation NPCs to Dopaminergic/Midbrain Neurons
By onThis protocol details methods for differentiation of NPCs to Dopaminergic/Midbrain Neurons. This 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)
pU6-pegRNA-LRRK2-G2019S-3c
By onIt can be used to introduce LRRK2-G2019S mutation using prime editing.
Protein network analysis links the NSL complex to Parkinson’s disease via mitochondrial and nuclear biology
By onA bioinformatics approach was taken to investigate the proteome of the NSL complex, to unpick its relevance to PD progression. The authors’ data points to NSL complex members OGT and WDR5 as key drivers of this increased PD association.
Immunofluorescence Staining
By onThe protocol describes immunofluorescence staining on brain sections.
Splicing accuracy varies across human introns, tissues and age
By onThis in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
fcs files to “The extracellular chaperone Clusterin enhances Tau aggregate seeding in a cellular model”
By onDataset associated with DOI: 10.17617/3.51VXU0
