Protocol Archive

Protocol for processing mouse tissue for immunohistochemistry.

hPSC Passaging and propagation using Laminin521 and EDTA. Laminin actively supports survival, prevents spontaneous differentiation, and increases plating efficiency, thus net expansion, and enables 100% confluent single cell layer epithelial monolayer culture. EDTA-based (Gentle Cell Dissociation Reagent) minimizes stress and enhances viability. Cell lines require little or no adaptation.

Staining of mouse brain sections with immunofluorescent visualization.

Protocol for imaging using confocal microscope. Sections for analysis should be mounted on slides, stained for appropriate markers, and coverslipped. This protocol uses a Carl Zeiss LSM 880 confocal microscope.

Protocol for imaging using Hamamatsu NanoZoomer slide scanner. Sections for analysis should be mounted on slides, stained for appropriate markers, and coverslipped. This protocol uses a Carl Zeiss LSM 880 confocal microscope.

Protocol for counting cells labeled with immunofluorescent markers in mouse brain sections. Sections should be stained, mounted, and imaged with high resolution (2048 x 2048 scanning).

Test for motor ability in mice.

This protocol describes the procedure for DNA extraction of saliva samples using the Omnigene OM device and the Qiagen QiaMP Powerfecal DNA PRO kit for shotgun metagenomic sequencing.

Protocol for processing 30um mouse brain sections for immunolabeling.

Nova-ST is an open-source, high-resolution sequencing-based spatial transcriptomics workflow. This method gives comparable resolution to BGI Stereoseq, SeqScope & PIXEL seq. Nova-ST is derived from dense nano-patterned randomly barcoded Illumina NovaSeq 6000 S4 sequencing flow cells.

This protocol describes the steps for extracting nuclei from human postmortem brain samples, immunofluorescence, and nuclei sorting (FANS) for single-nucleus RNA-seq using the Smart-Seq2 method.

This 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).

This 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 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.

This protocol details the multiplex labeling of free-floating tissues using tyramide fluorophores in the Killinger Lab (2024).

Using Oxford Nanopore MinION and the Rapid Barcoding library preparation kit, the authors perform long-read sequencing on droplet multiple displacement amplification (dMDA) products generated from single nuclei.

Alpha-synuclein phosphorylated at serine 129 (PSER129) occurs in two pools, non-aggregated (physiological) and aggregated (disease). This protocol allows for the selective dephosphorylation of non-aggregated PSER129 and enhances the specificity and sensitivity immunodetection of aggregated PSER129. Thus, this protocol can be used to differentiate physiological from aggregated PSER129.

The authors adapted the SureSelect XT HS2 DNA protocol to prepare libraries using as input material samples after single-cell Whole Genome Amplification (scWGA), instead of genomic DNA samples, for library preparation for Illumina single-cell Whole Genome Sequencing (scWGS).

The authors propose the use of LPS as a positive control for microglia activation assays (e.g., phagocytosis assay, cytokine production, and secretion), and as a phenotyping tool to investigate disease-mutated microglia by comparing to disease-relevant stimuli.

Here, the protocol describes a highly efficient method for differentiating monocytes/macrophages from hiPSC.