Fluorescence-activated nuclei sorting (FANS) for single-cell Whole Genome Sequencing (scWGS)
By Emma Sherrell onThis protocol describes the isolation steps of nuclei from human post-mortem brain samples, immunofluorescence, and nuclei sorting (FANS) for low coverage (<1x) single-cell Whole Genome Sequencing (scWGS) to detect mega-base somatic Copy Number Variations (CNVs).
The SATB1-MIR22-GBA axis mediates glucocerebroside accumulation inducing a cellular senescence-like phenotype in dopaminergic neurons
By Emma Sherrell onIn this study, the authors utilized human and murine neuronal lines, stem cell-derived dopaminergic neurons, and mice to demonstrate that three previously identified genetic risk factors for PD, namely SATB1, MIR22HG, and GBA, are components of a single gene regulatory pathway.
TNF-NF-κB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons
By Emma Sherrell onThe authors identified p53-mediated apoptotic cell death as a major contributor to dopamine neuron loss and uncovered a causal link of TNFa-NFκB signaling in limiting cell survival.
Saliva metagenomic data related to “Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics”
By Emma Sherrell onIn this study, the authors proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer.
scNAT Data for “scNAT: A deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles”
By Emma Sherrell onData for "scNAT: A deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles" publication.
Alpha-synuclein aggregates are phosphatase resistant
By Emma Sherrell onPhosphorylation of αsyn at serine 129 (PSER129) was considered rare in the healthy human brain but is enriched in pathological αsyn aggregates and is used as a marker for disease inclusions. Recent observations challenge this assumption. The authors investigated conditions under which PSER129 could be detected in the mammalian brain.
Available ASAP-related hPSC collection from Team Studer
By Emma Sherrell onCollection of human pluripotent stem cell lines from Team Studer consisting of isogenic GBA, LRRK2, SNCA series across three genetic backgrounds, KI-reporter lines for TOMM20 for mitochondria, b-actin for cytoskeleton, LAMB1 for cell membrane and LAMP1 for lysosomes, a-synuclein overexpression lines for Lewy body-like aggregation models, and other hPSC resources.
Nigrostriatal tau pathology in parkinsonism and Parkinson’s disease
By Emma Sherrell onHere, the authors demonstrate that loss of nigral dopaminergic neurons, loss of putamenal dopaminergic innervation, and loss of the tyrosine hydroxylase-phenotype in the substantia nigra and putamen occur equally in mild motor deficit groups with and without nigral alpha-synuclein aggregates.
Gut-initiated alpha synuclein fibrils drive Parkinson’s disease phenotypes: Temporal mapping of non-motor symptoms and REM sleep behavior disorder
By Emma Sherrell onThis study assesses the complex connections between α-synucleinopathies, gut-brain connectivity, and the emergence of non-motor phenotypes.
MERFISH dataset of mouse dopamine neurons
By Emma Sherrell onCell_by_gene and Cell_metadata files from MERFISH runs of mouse Midbrain spatial transcriptomics. Datasets are set up to be analyzed using Seurat v5.
Gut instincts in neuroimmunity from the eighteenth to twenty-first centuries
By Emma Sherrell onIn this review, the authors revisit the history of gut-brain interactions in science and medicine, which dates back to at least the eighteenth century, and outline how concepts in this field have shifted and evolved across eras.
scNAT: A deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles
By Emma Sherrell onThe authors developed scNAT, a deep learning method that integrates paired scRNA-seq and scTCR-seq data to represent data in a unified latent space for downstream analysis.
An open source head-fixation and implant-protection system for mice – Dataset
By Emma Sherrell onThe authors present a suite of open source, customizable head fixation designs with standard variants including head-fix hardware as well as implant protection systems.
Purification of proteins from PFA-fixed samples
By Emma Sherrell onThis protocol details the purification of proteins from PFA-fixed samples and the extraction of proteins from formalin-fixed tissues. Also includes the biotin pulldown prior to LC-MS/MS. Samples generated for this protocol have been used for mass spectrometry, immunoblotting, and pulldowns.
Rotarod
By Emma Sherrell onRotarod protocol optimized for mice. This test is made to assess motor coordination and balance. The results should show lower latency-to-fall numbers for mice with motor impairments.
Neither alpha-synuclein fibril strain nor host murine genotype influences seeding efficacy
By Emma Sherrell onFor unclear reasons, PD patients with certain GBA1 mutations (GBA-PD) have a more aggressive clinical progression. The authors tested the two hypotheses for why this occurs; that GBA1 mutations promote αsyn spread or drive the generation of highly pathogenic αsyn polymorphs (i.e., strains).
Pathogenic LRRK2 mutations cause loss of primary cilia and Neurturin in striatal Parvalbumin interneurons
By Emma Sherrell onThe authors show that Parvalbumin interneurons that are inhibitory regulators of movement also lose primary cilia.
Restoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s linked-LRRK2 mutant mice
By Emma Sherrell onParkinson’s disease-associated, activating mutations in LRRK2 block primary cilia formation, decreasing the production of neuroprotective factors that support dopaminergic neuron viability. The authors show that pathogenic LRRK2-driven cilia loss is reversible in post-mitotic neurons and astrocytes.
Primary data associated with the manuscript, “Restoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s linked-LRRK2 mutant mice” (doi: 10.1101/2024.07.31.606089)
By Emma Sherrell onPrimary data associated with the manuscript, "Restoration of striatal neuroprotective pathways by kinase inhibitor treatment of Parkinson’s linked-LRRK2 mutant mice." (doi: 10.1101/2024.07.31.606089)
Multiplex labeling with tyramide fluorophores (Free-floating tissues) – Killinger Lab 2024
By Emma Sherrell onThis protocol details the multiplex labeling of free-floating tissues using tyramide fluorophores in the Killinger Lab (2024).