Bulk RNA sequencing analysis
By onThis protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
Primary data associated with the manuscript “Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content” (doi.org/10.1101/2022.11.22.517583)
By onRaw data files used for the manuscript "Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content" (doi.org/10.1101/2022.11.22.517583).
Expression and purification for cryo-EM samples of FIP200NTD:ATG13(363-517)-ULK1(MIT) complexes
By onProtocol describing expression and purification protocols for cryo-EM samples of FIP200NTD:ATG13(363-517)-ULK1(MIT) complexes.
EPSCs source data across different simulation intensities of thalamus PT, IT neurons, and SC PT neurons
By onSource data compares EPSCs in thalamus PT, IT neurons, and SC PT neurons between control and 6_OHD mice across varying simulation intensities.
Transcardiac Perfusion of Mouse for Brain Tissue
By onTranscardiac perfusion is a method used for clearing blood and preserving the mouse brain for immunostaining.
LRRK2RCKW Widefield fluorescence microtubule binding assay
By onThis assay uses TMR labeled LRRK2 or LRRK1 RCKW to measure binding to microtubules in vitro
Metabolomic and lipidomic data reported in doi.org/10.1073/pnas.2219953120 (Golgi-IP, a tool for multimodal analysis of Golgi molecular content)
By onMetabolomic and lipidomic data associated with doi.org/10.1073/pnas.2219953120 deposited in MetaboLights repository with identifier number MTBLS6511.
GUV assay
By onThis protocol describes the preparation of GUVs for the reconstitution of LC3 lipidation reaction through the steps of PI3P production by PI3KC3-C1, WIPI2 recruitment and LC3 lipidation with PE. Screen reader support enabled.
Collection of protocols of Team Deleidi used in the publication: “”LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease””
By onCollection of protocols of Team Deleidi used in the publication: ""LRRK2 kinase activity regulates GCase level and enzymatic activity differently depending on cell type in Parkinson’s disease""
H9 ES AAVS1-NGN2 FAM134C/A/B-/-;TEX264-/-; PiggyBac-Keima-REEP5
By onES cells modified to produce iNeurons w/o ER-phagy receptor FAM134C/A/B, TEX264, and with Keima-REEP5 reporter. CRISPR/Cas9 used to introduce NEUROG2 construct in AAVS1 locus. Knockouts RETREG1/2/3, TEX264. Transfected with NEUROG2, REEP5, mKeima.
Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content
By onThe authors develop a method for the rapid capture of intact Golgi via Golgi immunoprecipitation. Using high-resolution mass spectrometry, the approach allows the unbiased characterization of the Golgi proteome, metabolome, and lipidome.
pFastBac_Dual_GST-TEV-mCherry-TBK1
By onPlasmid: Plasmid for the expression and purification of GST-TEV-EGFP-TBK1 in Spodoptera frugiperda cells (Sf9). Internal reference: SMC1631. Used for the expression and purification of mCherry labelled TBK1 (SMC Internal No.: 1675).
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.
By onThe GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines (associated with publication 10.1101/2022.06.01.494130).
Whole-cell Patch-Clamp Recordings from Striatal Cholinergic Interneurons in ex vivo Mouse Brain Slices
By onProtocol for patch-clamp recording of mCherry-labelled striatal ChIs from mouse brain slices with added step for labelling astrocytes using SR101.
Luminescent Conjugated Oligothiophenes (LCO) Staining
By onThe protocol describes Luminescent Conjugated Oligothiophenes staining on brain sections.
Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system
By onModern neuroscience approaches including optogenetics, calcium imaging, and other genetic manipulations have facilitated our ability to dissect specific circuits in rodent models to study their role in neurological disease. These approaches regularly use viral vectors to deliver genetic cargo (e.g., opsins) to specific tissues and genetically-engineered rodents to achieve cell-type specificity. However, the translatability of these rodent models, cross-species validation of identified targets, and translational efficacy of potential therapeutics in larger animal models like nonhuman primates remains difficult due to the lack of efficient primate viral vectors. A refined understanding of the nonhuman primate nervous system promises to deliver insights that can guide the development of treatments for neurological and neurodegenerative diseases. Here, we outline recent advances in the development of adeno-associated viral vectors for optimized use in nonhuman primates. These tools promise to help open new avenues for study in translational neuroscience and further our understanding of the primate brain.
Generation of stable ATG3-mCherry wild-type or mutans HeLa cells with HaloTag-LC3B using lentivirus
By onThis protocol details the generation of stable ATG3-mCherry wild-type or mutant HeLa cells with HaloTag-LC3B using lentivirus.