Protocol Archive

Protocol for 3' mRNA sequencing of mouse gastrointestinal tract tissues.

Protocol for mouse gastrointestinal function assays (whole gut transit time, fecal water content, and fecal output).

Methods to measure deflection characteristics of carbon fiber electrodes in agar brain phantoms.

Protocol for ex vivo assay of colonic migrating motor complexes (CMMCs) in mouse colons.

QuPath is a bioimage analysis software designed for digital pathology and whole slide image analysis. This protocol describes how to measure CD8 density in the substantia nigra and cerebral peduncle using haematoxylin and DAB-stained brain sections.

This is the protocol for assessing cell viability using a MTS cell proliferation assay kit.

This protocol describes the evaluation of cellular processing of GPNMB mutants by Western Blotting and Immunofluorescent imaging in a HEK293 overexpression model.

This protocol details methods for 3-day Mitochondrial Antigen Presentation Assay in a murine macrophage cell line (RAW) that expresses a glycoprotein B (gB) of herpes simplex virus 1 (HSV1) targeted to the mitochondrial matrix (mito-gB). Watch an interview about this protocol with Ahmed Fahmy, PhD. 

A protocol for differentiating AAVS1-TRE3G-NGN2 hESCs to iNeurons directly on EM grids for cryo-ET and cryo-CLEM. The protocol includes: (1) EM grids coating with Matrigel or Poly-Ornithine and Laminin; (2) differentiation and seeding of iNeurons on EM grids; (3) lentiviral transduction for transient expression of fluorescently-labeled proteins; and (4) plunge freezing. Watch an interview about this protocol with Cristina Capitanio, MSc. 

In this protocol, the authors describe the preparation and maintenance of rat organotypic cultures from parasagittal brain slices.

FASTQ alignment, gene counts, and differential expression analysis and functional annotation of DEGs.

Patient PBMC flow cytometry.

Patient PBMC differentiation to macrophages.

pH-Rodo pathogens to monitor phagocytosis in pMacs.

DQ-BSA and BMV109 microscopy for peritoneal macrophages.

Ea(52-68) uptake assays on pMacs.

This protocol details methods for structural determination by transmission electron cryo-microscopy of 20S CPs and assembly intermediates.

Flow cytometry for ex vivo stimulated pMacs.

This protocol details methods for cloning, expression, and purification of 20S CPs, and assembly intermediates for biochemical and structural analysis.

This protocol details how to efficiently monitor Tau aggregation by thioflavin-T fluorescence in a plate reader.