📅 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
