Code for integrated multi-cohort analysis of the Parkinson’s disease gut metagenome
By onDetailed scripts to reproduce all analysis and data visualization for the paper "Integrated multi-cohort analysis of the Parkinson's disease gut metagenome."
Regulatory imbalance between LRRK2 kinase, PPM1H phosphatase, and ARF6 GTPase disrupts the axonal transport of autophagosomes
By onThe authors found that LRRK2-hyperphosphorylated RABs disrupt the axonal transport of autophagosomes by perturbing the coordinated regulation of cytoplasmic dynein and kinesin motors.
Deep Brain Stimulation (DBS) Implant
By onThis protocols describing the steps for making implants used for deep brain stimulation (DBS) in rodents.
pCAG- WIPI2dR108E- cs-TEV -STREP
By onPlasmid for mammalian expression of human WIPI2d R108E with C-terminal Strep.
Tet-off TauRD (HEK293T)
By onAssociated with the following preprint: Saha et al., 2022 (published on biorxiv on Feb 19th, 2022) https://www.biorxiv.org/content/10.1101/2022.02.18.481043v1.full
Expression and purification protocol of GST-TAX1BP1
By onThis protocol details the expression and purification protocol of GST-TAX1BP1.
In vitro kinase assay: phosphorylation of PI3Kc1 by TBK1and ULK1
By onProtocol describing in vitro kinase assay, in which PI3Kc is tested for phosphorylation by TBK1 and ULK1 complex either by western blotting (S29 on ATG14L subunit) or mass spectrometry analysis.
H9 ES AAVS1-NGN2 FAM134A-/-; PiggyBac-Keima-RAMP4
By onES cells were modified to create iNeurons lacking FAM134A and expressing Keima-RAMP4 ER-phagy flux reporter. CRISPR/Cas9 was used to introduce NEUROG2 construct in AAVS1 locus. Transfected with Keima-RAMP4 vector.
Automated Immunohistochemistry Staining
By onThe protocols describe the steps for automated immunohistochemistry staining using the Ventana Discovery® XT Immunostainer.
iPS Cell line CRICKi011-A (iFCI016), c.G152A mutation in Exon 3 of SNCA
By onMutations in the SNCA gene cause rare autosomal dominant Parkinson’s disease. iPSC lines were created from individuals with SNCA G51D mutations, showing potential for disease modeling and therapy development for synucleinopathies.
Acute striatal or midbrain fiber photometry in head-fixed mice
By onWhile this protocol focuses recordings from striatum with GCaMP, it can be easily modified to record from other brain regions and with other fluorescent reporters.
Standard Operating Procedure: Mouse transcardiac perfusion protocol
By onMouse transcardiac perfusion protocol and storage.
Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures–Gene Validation FCS
By onFCS files corresponding to the gene validation experiment described in "Transcriptional analysis of peripheral memory T cells reveals Parkinson’s disease-specific gene signatures"
pAC150-Keima-REEP5
By onSummary: Piggybac vector used to express Keima-REEP5 autophagy flux reporter, a tool to monitor autophagy flux in cells by measuring pH changes in autophagosomes and lysosomes.
Immunofluorescence staining for postmortem mouse brain tissue
By onThis is a basic protocol for staining mouse brain tissues using immunofluorescence and immunohistochemistry techniques.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt
By onThe authors developed a functional proteomics framework, termed MitoPQ (Mitochondrial Proteostasis Quantification), to dissect the UPRmts role in maintaining proteostasis during stress.
CRISPR tagging of the EEA1 gene in H9 ES cells for Endo-IP
By onProtocol for tagging EEA1 gene in human H9 ES cells with a 3X flag using CAS9 and oligonucleotide template is described.
