Boles_et-al_DSS_time-series
By Emma Sherrell onProcessed and normalized counts after the removal of low-quality genes and samples. These data are separated into colon ("colon_clean_VST_counts.csv") and brain ("brain_clean_VST_counts.csv"). The sample key can be found in the metadata at the GEO entry page. This repository contains the code that was used to generate these cleaned counts from the raw counts.
Examining the brain’s response to intestinal permeability and inflammation in the dextran sulfate sodium-induced colitis model
By Emma Sherrell onFrom the brain, cortex, hippocampus, ventral midbrain, and striatum were taken to examine both global and regionally-specific transcriptomic perturbances that emerge in response to gut leakiness. All tissues were assayed with high-throughput RNA sequencing.
Gut mucosal cells transfer α-synuclein to the vagus nerve
By Emma Sherrell onPublished: These findings highlight a potential non-neuronal source of fibrillar α-synuclein protein that might arise in gut mucosal cells. View original preprint.
DAB antibody (IHC) staining protocol
By Emma Sherrell onThis is the basic protocol for antibody staining of formalin fixed paraffin embedded (FFPE) tissue. This is the basic protocol for antibody staining of formalin fixed paraffin embedded (FFPE) tissue.
Comparative analysis of methods to reduce activation signature gene expression in PBMCs
By Julia Julia Leonard onPreprint: These findings highlight the importance of considering the advantages and drawbacks of different isolation methods to ensure accurate interpretation of PBMC transcriptomic profiles.
VPS13B is localized at the cis-trans Golgi complex interface and is a functional partner of FAM177A1
By Julia Julia Leonard onPreprint: These findings raise the possibility that bulk lipid transport by VPS13B may play a role in expanding Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
A STING-CASM-GABARAP pathway activates LRRK2 at lysosomes
By Julia Julia Leonard onPreprint: These results define a pathway that integrates multiple stimuli at lysosomes to control the kinase activity of LRRK2. Aberrant activation this pathway may be of relevance in both Parkinson’s and Crohn’s diseases.
Lysosomal TBK1 responds to amino acid availability to relieve Rab7-Dependent mTORC1 inhibition
By Julia Julia Leonard onPreprint: Data establishes the lysosome as a site of amino acid regulated TBK1 signaling that is crucial for efficient mTORC1 activation. This lysosomal pool of TBK1 has broader implications for lysosome homeostasis, and its dysregulation could contribute to the pathogenesis of ALS-FTD.
Intramuscular PFF injection
By Emma Sherrell onThis protocol details the intramuscular PFF injection procedure. This protocol details the intramuscular PFF injection procedure.
Synthesis of 1-(3-Chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione
By Julia Julia Leonard on1-(3-chlorophenethyl)-3-cyclopentylpyrimidine-2,4,6-(1H,3H,5H)-trione (8) is a potent and highly selective Ca(V)1.3 L-type calcium channel antagonist. This protocol is an adaption of Kang et al., 2012's method of the synthesis of this chemical.
Open field
By Emma Sherrell onThis protocol details about Open Field procedure. This protocol details about Open Field procedure.
A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy
By Julia Julia Leonard onPreprint: Cortical axons in conduits are severed by a media jet; then, brain-derived neurotrophic factor and striatal neurons in distal chambers promote axon regeneration. As additional conduits and chambers are easily added, this opens up the possibility of mimicking complex neuronal networks and screening drugs for their effects on connectivity.
AAV injection in the nodose ganglia of mouse
By Emma Sherrell onThe study of these ganglia is challenging in small animals due to size and location. Hence, in this protocol, the team describes a practical surgical approach to the vagal trunk, and the JNG complex in mice.
Automatic flow in fluid-walled dumbbells driven by Laplace pressure
By Julia Julia Leonard onThis protocol describes experiments performed to quantify pressure and volume variations inside fluid-walled dumbbells when a pressure difference is generated between the two chambers. Difference in Laplace pressure automatically flows medium from the high-pressure chamber to the low pressure one. Flow stops when pressures are equilibrated.
Immunostaining of corticostriatal culture on fluid-walled dumbbells
By Julia Julia Leonard onThis protocol describes the immunocytochemistry of the iPSC-derived corticostriatal culture on fluid-walled dumbbells.
Fura-2 imaging of ionomycin response, with and without R568; a CaSR positive modulator
By Julia Julia Leonard onFura-2 imaging protocol to accompany Kilfeather, Khoo et al., 2023: Single cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease.
Generation of stable cell lines using retroviral system
By Emma Sherrell onThis protocol details generation of stable cell lines using retroviral system.