| Day 1 |
Morning Session: Introduction, Sample Handling and Contamination Control |
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Introduction to experimental workflows; contamination prevention strategies; sample tracking, labeling, and pipetting best practices.
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| Afternoon Session: Cell Preparation Workflows |
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Preparation of cultured cells and tissue-derived samples; cell counting and viability assessment; optimization of cell handling prior to downstream chromatin assays.
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| Evening Session: Quality Control using Microscopy |
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QC assessment using brightfield and fluorescent microscopy; evaluation of cell integrity and sample quality; troubleshooting common preparation artifacts.
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| Day 2 |
Morning Session: Introduction to CUT&Tag + Guest Lecture |
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Overview of CUT&Tag principles and workflow; discussion of chromatin profiling strategies; external expert lecture on applications, experimental design, and common technical pitfalls.
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| Afternoon Session: CUT&Tag – Cell Preparation |
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Cell preparation and immobilization; permeabilization workflows; optimization of sample handling and permeability prior to antibody incubation.
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| Evening Session: Washes and Primary Antibody Binding |
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Wash steps to minimize background signal; primary antibody incubation; troubleshooting antibody specificity and sample quality issues.
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| Day 3 |
Morning Session: Secondary Antibody Binding and pA-Tn5 Incubation |
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Secondary antibody incubation; pA-Tn5 binding and handling; optimization of reaction conditions and reduction of non-specific background.
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| Afternoon Session: Tagmentation and Library Amplification |
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Tagmentation activation and cleanup steps; PCR amplification and indexing strategy; optimization of amplification cycles and library yield.
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| Evening Session: Library QC and Troubleshooting |
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Assessment of library concentration and fragment profiles; identification of low-yield or over-amplified libraries; troubleshooting and preparation for downstream sequencing.
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| Day 4 |
Morning Session: Introduction to ATAC-seq + Guest Lecture |
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Overview of ATAC-seq principles and chromatin accessibility profiling; external expert lecture on experimental design, applications of ATAC-seq, and common technical challenges in open chromatin analysis.
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| Afternoon Session: Nuclei Isolation and Transposition Reaction |
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Nuclei isolation workflows and quality assessment; transposition reaction setup; optimization of nuclei handling and reduction of sample debris.
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| Evening Session: Library Amplification and QC Metrics |
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Library amplification and fragment enrichment; interpretation of nucleosomal periodicity patterns; troubleshooting library quality and yield issues.
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| Day 5 |
Morning Session: Library QC using TapeStation |
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Fragment size distribution analysis; identification of successful vs failed libraries; pooling logic, sequencing readiness, and troubleshooting discussion.
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| Afternoon Session: Workshop Review, Feedback and Closing Remarks |
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Review of workflows and troubleshooting strategies covered during the workshop; participant feedback session; discussion on implementation in home laboratories; certificate distribution and closing remarks.
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