Oxford Nanopore Sequencing for 3D Organoid Models: Hands-on Long-Read Transcriptomics and Bioinformatics
Decode 3D organoid biology using Oxford Nanopore long-read sequencing and practical bioinformatics workflows.
Skills you will gain:
About Program:
Organoid models provide physiologically relevant 3D systems for studying tissue development, disease modeling, and drug response. Coupling these with Nanopore long-read sequencing enables full-length transcript and structural variant analysis in a biologically faithful context.
This workshop guides participants through the entire workflow—from organoid prep and nucleic acid extraction to Nanopore sequencing, data acquisition, and bioinformatics analysis. Emphasis is placed on hands-on computational and instrument training, allowing participants to confidently generate and interpret high-quality long-read data from complex 3D models.
Aim: Learn to combine 3D organoid biology with Oxford Nanopore long-read sequencing for high-quality nucleic acid analysis.
Gain practical skills in sample prep, library construction, and bioinformatics pipelines for organoid-based research.
Program Objectives:
Participants will learn to:
- Prepare 3D organoid cultures and extract high-quality HMW DNA and RNA.
- Perform Nanopore QC and platform setup for sequencing.
- Construct Nanopore libraries using ligation or rapid prep kits.
- Deploy Nanopore bioinformatics pipelines (Minimap2, EPI2ME Labs) for long-read data.
- Analyze and interpret read-length distributions, isoforms, and structural variants.
What you will learn?
📅 Day 1: Organoid Prep & Nanopore-Ready Nucleic Acid Extraction
- Core Objective: Understand how 3D organoid models are prepared for high-quality Nanopore long-read sequencing workflows.
- Overview of 3D cellular models, including cerebral organoids, intestinal organoids, and tumoroids
- Nanopore long-read advantage for full-length isoforms and structural variant analysis
- Dissolving extracellular matrices such as Matrigel without affecting sample quality
- Extracting High-Molecular-Weight DNA and intact RNA for Nanopore sequencing
- Sample quality control for purity, quantity, and sequencing readiness
🛠️ Hands-on:
- Hands-on Lab: Navigating the Nanopore MinKNOW GUI and running flow cell platform QC
🧰 Tools Covered: MinKNOW, ONT Flow Cell QC, Organoid Sample QC Concepts
📅 Day 2: Nanopore Library Preparation Chemistry & Sequencing Physics
- Core Objective: Learn how Nanopore library preparation chemistry and sequencing physics support real-time long-read data generation.
- Choosing the right Nanopore library kit: ligation-based vs. rapid preparation workflows
- Digital fluidics mapping using the official Oxford Nanopore Protocol Builder
- Structuring Nanopore library preparation workflows inside Benchling
- Understanding Nanopore biophysics and ionic current disruption during sequencing
- Real-time processing with Dorado Basecaller using high-accuracy and super-accuracy models
🛠️ Hands-on:
- Hands-on Tool: Build and map a Nanopore library preparation workflow using ONT Protocol Builder
🧰 Tools Covered: ONT Protocol Builder, Benchling, Dorado Basecaller
📅 Day 3: Nanopore Bioinformatics Pipelines & Downstream Analysis
- Core Objective: Analyze Nanopore sequencing outputs through alignment, visualization, workflow automation, and downstream interpretation.
- Understanding native Nanopore output formats: POD5, FASTQ, and BAM
- Mapping Nanopore long reads using Minimap2 alignment workflows
- Launching automated organoid analysis workflows through Nanopore EPI2ME Labs
- Interpreting read-length N50, isoforms, variants, and sequencing output quality
- Troubleshooting Matrigel contamination and preventing Nanopore flow cell clogging
🛠️ Hands-on:
- Hands-on Lab: Run Nanopore bioinformatics workflows and interpret long-read sequencing results using EPI2ME Labs
🧰 Tools Covered: POD5, FASTQ, BAM, Minimap2, EPI2ME Labs
Mentor Profile
Fee Plan
Get an e-Certificate of Participation!
Intended For :
- Undergraduate/postgraduate degree in Biotechnology, Molecular Biology, Bioinformatics, Genetics, Cell Biology, or related fields.
- Researchers or professionals in 3D cell culture, genomics, transcriptomics, and single-cell biology.
- Individuals interested in long-read sequencing applications in organoid research.
Career Supporting Skills
Program Outcomes
- Gain practical knowledge of organoid prep and nucleic acid extraction.
- Operate Nanopore instruments and perform flow cell QC and library prep.
- Process and align long-read data using Minimap2 and cloud pipelines.
- Visualize and interpret sequencing metrics (read length, isoforms, variants).
- Troubleshoot common issues like Matrigel contamination and flow cell clogging.