EDDU: Resources for Researchers


We combine our capabilities with those of our partners to:

  1. Use induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to study the molecular basis of neurological diseases
  2. Develop new tools and technology in disease modelling and target engagement that will help to identify potential therapies
  3. Translate newly developed assays onto an automated high-throughput platform that can be integrated with preclinical drug screens

Mini brain in petri dish, seen on video screen

Multidimensional iPSC-derived models

  • 2D models: Neurons (cortical, dopaminergic, motor, sensory), astrocytes, oligodendrocytes, and microglia
  • 3D models: Forebrain organoids, cerebral organoids, midbrain organoids

Mini brain as seen under microscope

Robust disease models

  • iPSCs from healthy individuals and from patients with neurological disorders
  • Core areas include Parkinson’s disease, Amyotrophic Lateral Sclerosis (ALS), and intellectual disability/autism spectrum disorders

Organoid as viewed under microscope.

Quality control

  • Industry-level standard operating procedures (SOPs)
  • Established quality control pipeline
  • Comprehensive one-on-one and group training offered in-house and sponsored by STEMCELL Technologies


Carol Xiuqing Chen leads the  iPSC phenotyping and CRISPR editing Working Group.

iPSC phenotyping and CRISPR editing

iPSCs are at the heart of research at the EDDU.

This working group is responsible for characterizing iPSC lines that come through the EDDU to ensure that only high-quality iPSCs are used in our research projects. The group is further expanding their library of iPSC lines by generating gene-edited versions using CRISPR technology.

iPSC phenotyping

  • Optimization of growth media and passaging reagents
  • Quality control testing including chromosomal integrity, morphological features, pluripotency marker expression, microbiological/viral screening

CRISPR editing

  • Genetic knockin or knockout (KO) in control lines
  • Correction of disease-associated mutations in patient lines

Antibody Validation and CRISPR KO

Mathilde Chaineau is part of the Discovery assays and screens Working Group.

Discovery assays and screens

Automation is driving research forward at the EDDU.

With state-of-the-art equipment, this group is working to bring our assays with iPSC-derived cells into  screenable 2D and 3D formats.

"In-house" tools for image acquisition and analysis

  • Optimization of immunofluorescence-based assays
  • Established workflow for data management
  • Open-source software developed in house to enhance data analysis

Focus on multiple disease areas:

  • Parkinson’s disease and other synucleinopathies
  • Neuromuscular diseases
  • Neurodevelopmental diseases
  • Neuroimmune and Neuroinflammation

Researcher leaving notes on plexiglass to share information.

Brain Organoids and tissue engineering

3D neuronal Organoids are shaking up our perspective on the human brain.

Taking iPSC-derived neurons beyond two dimensions has allowed this group to establish the EDDU’s organoid program. The team is applying multiple approaches to characterize 3D neuronal organoid models, while also exploring innovative 3D culturing systems.

3D model development

  • Multiple tissue types: forebrain, midbrain, cerebral
  • Customizable batch numbers (100 to 700) and age (15 days to 100+ days)

Histology and 3D imaging

  • Immunohistochemistry and immunofluorescence microscopy
  • Parafilm embedding and microtome sections
  • Cubic tissue clearing
  • Methods for automated 3D imaging on Opera Phenix HCs

Organoid maintenance and quality control

  • 15K minibrain capacity in organoid-specific incubators
  • Dedicated team oversees day-to-day monitoring of each individual organoid using a Laboratory Information Monitoring System (LIMS)

Single cell phenotyping

  • Comprehensive analysis of individual cell types in organoids using our state-of-the-art, automated Attune Acoustic Flow Analyzer
  • Workflow for isolation of single cells from organoids for flow analysis or single-cell sequencing analysis
  • Informatics pipeline for handling single-cell expression data of specific cell types within organoids

Researcher with student

Training and outreach

Train and learn with us at the EDDU.

Our Training and Outreach working group is involved in a variety of activities designed to help researchers learn how to use iPSCs in their projects, and to provide opportunities for them to engage with others in the iPSC field.

“Introduction to iPSCs” hands-on workshops

One-on-one hands-on training

  • Intensive hands-on instruction offered by our iPSC experts

Open protocols

  • Development of openly available protocols for culturing iPSCs and differentiating iPSCs into specific cell types

iPSC Seminar Series

  • Bi-monthly seminars by trainees and leading experts in the field
  • Sponsorship provided by STEMCELL Technologies

Undergraduate training opportunities

  • Opportunities for undergraduate students to work within the EDDU
  • Mentored by senior researcher with opportunities for projects from stem cells to developing image analysis software. Contact lenore.beitel [at] mcgill.ca (Dr. Lenore Beitel) for further information on how you can join the team. 

Watch for news on upcoming workshops and seminars on our Open Science Events feed.



Read blog posts from Thomas Durcan, the EDDU’s Associate Director, on his Open Lab Notebook.

Blog icon
Thomas Durcan's Open Lab Notebook | Read the notebook |Meet Tom


Read our protocols to learn from our experience. Our protocols are open and freely available for download from Zenodo.

  • PDF download
    Culture Reagents
    Interactive PDF

  • PDF download
    iPSC Culture
    Static PDF
    Interactive PDF

  • PDF download
    Motor Neuron Induction and Differentiation
    Static PDF
    Interactive PDF

  • PDF download
    Dopaminergic or Cortical Neuron Differentiation
    Static PDF
    Interactive PDF

  • SeqStudio DNA Sequencing
    Static PDF

  • Production of Recombinant α-Synuclein Monomers and Preformed Fibrils (PFFs)
    Static PDF

  • Quality Control Characterization of α-Synuclein Preformed Fibrils (PFFs)
    Static PDF

  • PDF download
    Dopaminergic or Cortical Neural Progenitor Cell Induction
    Static PDF

  • CRISPR-mediated introduction of single nucleotide changes in iPSCs
    Static PDF

  • Generation of Knockout Cell Lines Using CRISPR-Cas9 Technology
    Static PDF

  • High Content Imaging, Analysis and Data Management
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  • Generation of OPCs and Oligodendrocytes from iPSCs
    Static PDF
    Interactive PDF

  • Generation of Knockout Cells Using CRISPR and ddPCR Technology
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  • Sequencing Analysis Guide
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  • Generation of Forebrain Spheroids
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  • Synuclein uptake assay in iPSC-derived DA NPCs
    Static PDF

Publications & Posters

Read our publications and the posters we have presented at scientific meetings. Our publications and posters are open and available for download.

  • PDF download
    Patient-Derived Stem Cells, Another in vitro Model, or the Missing Link Toward Novel Therapies for Autism Spectrum Disorders?
    Link to publication

  • PDF download
    One Step Into the Future: New iPSC Tools to Advance Research in Parkinson's Disease and Neurological Disorders
    Link to publication

  • PDF download
    Disruption of GRIN2B Impairs Differentiation in Human Neurons
    Link to publication

  • PDF download
    Open Science Meets Stem Cells: A New Drug Discovery Approach for Neurodegenerative Disorders
    Link to publication

  • PDF download
    The Neuroprotective Role of Protein Quality Control in Halting the Development of Alpha-Synuclein Pathology
    Link to publication

  • PDF download
    Standardized quality control workflow for analyzing the quality and differentiation potential of human iPSCs
    Static PDF

  • PDF download
    Generation of human midbrain organoids from induced pluripotent stem cells
    Link to publication

  • PDF download
    Using stem cells to study the effects of cannabis on neuronal development
    Link to publication

  • Implementation of an Antibody characterization pipeline- McPherson lab
    Link to publication

  • Characterization of the activity-dependent development of IPSC-derived neurons from Fragile X patients
    Static PDF

  • Quantitative characterization of variability in cortical neurons between healthy human induced pluripotent stem cell lines
    Static PDF

  • Variability among iPSCs- Building a QC pipeline and how to predict good iPSCs for generating neurons- Till and McCulloch talk 2019
    Static PDF

  • The Quebec Parkinson Network: A Researcher-Patient Matching Platform and Multimodal Biorepository.​​​​​​
    Link to publication

  • Characterization of human iPSC-derived astrocytes with potential for disease modeling and drug discovery
    Link to publication

  • Defining the Neural Kinome
    Link to publication

  • Stimulation of L‐type calcium channels increases tyrosine hydroxylase and dopamine in ventral midbrain cells induced from somatic cells
    Link to publication

  • Characterization of human-iPSCs derived spinal motor neurons by single-cell RNA sequencing
    Link to publication

  • Quantitative expansion microscopy
    Link to publication


Use our software to accelerate your data analysis. Our software will be open and freely available for download.

  • Download software
    A Fiji macro for measuring organoid area and size
    Static PDF


Contact us to find out how our infrastructure can help you with your research.

Researcher working with Flow Cytometry equipment
Flow Cytometry and Fluorescence Activated Cell Sorting (FACS)

Analyze and sort cells in our dedicated flow facility.


Researcher working with high content screening equipment
Drug Discovery and Screening

Optimize cell-based assays and small molecule screens with our automated high-content screening (HCS) platform.

neuroeddu.mni [at] mcgill.ca (subject: Drug%20Discovery%20and%20Screening%3A%20Website%20enquiry) (Email us)


neuroeddu.mni [at] mcgill.ca (Contact us) about using our biological materials for your research, including:

Seminar Series

Contact irina.shlaifer [at] mcgill.ca (Irina Shlaifer) to join the mailing list for the iPSC Seminar Series and to let us know if you are interested in giving a talk.

Next seminars: Thursday September 24th, 4pm




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The Neuro is a McGill research and teaching institute; delivering high quality patient care, as part of the Neuroscience Mission of the McGill University Health Centre. We are proud to be a Killam Institution, supported by the Killam Trusts.




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