Genotyping mice from ear clips
By onThis protocol describes the genotyping procedure from ear clip samples. This includes a general PCR protocol for primers with annealing temperatures in the range 55-70 degrees C. For other primers, the thermal cycling should be adjusted.
Ectopic receptor & endosome size and count image analysis and quantification
By onThis protocol is to help with the imaging analysis of ectopic receptor localization and endosome size.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Fluorospot SFC
By onFluorospot SFC (combined IFNg, IL-5, and IL-10) data and corresponding HC-PD group IDs described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"
Generation of stable cell lines via lentiviral transduction
By onProtocol describing the generation of stable cell lines using a lentivirus system.
His-ATG3-K62D/K64D
By onPlasmid: ATG3 mutant overexpression in E.Coli. 6His-TEVsite-ATG3-K62D/K64D-stop.
Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics
By onThe authors developed an assay, Endo-IP, to rapidly isolate early and sorting endosomes. Using this method, they found a unique proteomic landscape of early/sorting endosomes, distinct from lysosomal proteomic landscape.
pCAG-OSF-ATG13 (2-197)-Y152D
By onPlasmid for expression of human ATG13 HORMA Y152D mutant in mammalian cells.
CMV mScarlet-LC3B
By onPlasmid: Mammalian expression of fluorescently-tagged marker for autophagic vesicles.
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).
