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A protocol for simultaneous high-sensitivity genotyping and chromatin accessibility profiling in single cells.

Sven Turkalj1, Niels Asger Jakobsen2, Angus Groom1

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Summary

This study introduces a novel method combining single-cell ATAC sequencing (scATAC-seq) with genotyping to analyze how somatic mutations affect chromatin accessibility. This integrated approach allows researchers to study epigenetic changes alongside genetic variations in single cells.

Keywords:
BioinformaticsCancerGeneticsGenomicsMolecular BiologySequence AnalysisSequencingSingle CellStem Cells

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Single-cell ATAC sequencing (scATAC-seq) reveals cell-to-cell epigenetic variations.
  • Current scATAC-seq methods do not typically detect exonic mutations.
  • Understanding the interplay between somatic mutations and chromatin is crucial.

Purpose of the Study:

  • To develop a method integrating high-sensitivity genotyping with scATAC-seq.
  • To enable simultaneous analysis of genetic mutations and chromatin accessibility in single cells.
  • To provide a detailed protocol for this combined single-cell assay.

Main Methods:

  • A plate-based protocol was developed for single-cell analysis.
  • Optimization of genotyping primers for specific genomic loci.
  • Preparation of both scATAC-seq and single-cell genotyping libraries.
  • Automation of library preparation using high-throughput liquid handling platforms.

Main Results:

  • Successful coupling of high-sensitivity genotyping with high-content scATAC-seq.
  • Demonstration of a method to analyze exonic mutations and chromatin landscapes simultaneously.
  • Detailed protocol guidance for researchers.

Conclusions:

  • The presented method overcomes limitations of standard scATAC-seq by incorporating genotyping.
  • This integrated approach facilitates the study of somatic mutation impacts on epigenetic states.
  • The protocol is optimized for high-throughput automation.