Induced Cortical Neuron Differentiation – Part 3 – Day 7 Dissociation
By onProtocol for replating neurons after seven days of cortical transdifferentiation and prepare cells for longer-term culture.
Seeded amplification assay (SAA) from neuronal cell or postmortem brain lysates
By onDetection of minute amounts of misfolded α-synuclein aggregates in neuronal cell lysates.
Western blot of amplified fibrils after Proteinase K digestion
By onProtocol for western blot of amplified fibrils of a-synuclein after proteinase K digestion.
Induced Cortical Neuron Differentiation – Part 2 – Day 0 Dissociation
By onProtocol to initiate differentiation of human iPS cells into cortical neurons by doxycycline induction of NGN2 transgene expression. Use iPSCs transfected with an NGN2-puroSNAP PiggyBac construct, with a blasticidin-resistance backbone.
Induced Cortical Neuron Differentiation – Part 1 – Overview
By onProtocol to differentiate human iPS cells into cortical neurons by doxycycline induction of NGN2 transgene expression. Use iPSCs transfected with an NGN2-puro-SNAP PiggyBac construct, with a blasticidin-resistance backbone.
Seahorse XF Cell Mito Stress Test
By onSeahorse XF Cell Mito Stress Test for assessment of oxygen consumption rate in iPSC-derived neurons as a measure of mitochondrial respiration.
Quantitative PCR for STMN2 expression in pi-N neurons
By onQuantitative PCR for STMN2 expression in pi-NSNCA-STMN2 neurons.
PFF seeding in U2OS cells
By onThis protocol describes the seeding of intracellular inclusions in U2OS cells harboring overexpressing a-synuclein via exogenous addition of short-length preformed a-synuclein fibrils.
Whole cell protein extraction and Western blotting
By onThis protocol describes cell lysis for whole-cell protein extraction followed by western blotting using LI-COR Odyssey quantitative western blot.
PFF seeding in iPSC-derived cortical neurons
By onHow to seed intracellular inclusions via exogenous addition of short-length pre-formed aSyn fibrils.
Proximity ligation assay
By onProximity ligation assay (PLA) in iPSC-derived cortical neurons. Permeabilization with Saponin detergent is used to preserve lipid-rich inclusions.
Generation of preformed αS fibrils
By onThis protocol describes the generation of wild-type recombinant alpha-synuclein preformed fibrils (PFFs).
Stable integration of piggyBac plasmids into U2OS cells
By onGeneration of stably transfected U2OS human osteosarcoma cell line with piggyBac constructs.
Mitochondrial subunit assay in hiPSC-derived neurons.
By onAssessment of mitochondrial subunit levels in hiPSC-derived neurons.
BIDCell to Seurat
By onThis repository contains an enabler script to convert the BIDcell segmentation output to a Seurat object for the processing of 10X Genomics Xenium spatial transcriptomics data.
Multiome preprocessing seurat
By onWorkflow to preprocess single nucleus multiome data (gene expression + ATAC) produced with 10X Genomics Cellranger ARC in Seurat.
TULIP – mulTiome demultiplexing Using Long-read SNP Information Pipeline
By onSnakemake pipeline to demultiplex 10x multiome data utilizing SNP calls from WGS sequencing of pooled patients.
Differentiation of WTC11 and KOLF2.1 iPSCs to dopaminergic neurons (forked)
By onThis protocol describes the differentiation of iPSCs (WTC11 and KOLF2.1) to dopaminergic neurons according to Bressan et al 2021.
Temporal control of acute protein aggregate turnover by UBE3C and NRF1-dependent proteasomal pathways
By onNeurodegenerative diseases involve proteostasis loss and protein aggregation leading to cell toxicity. Study reveals proteasome-dependent degradation of misfolded proteins, regulated by NRF1, UBE3C, and RPN13, impacting proteostasis in cells.
Neuronal co-culture
By onThis protocol describes the co-culturing of iPSC-derived dopaminergic (DA) neurons and iPSC-derived medium spiny neurons (MSNs) in a microfluidic compartmentalization device.
