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Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri.

G Adam Reeves1, Param Priya Singh1, Anne Brunet2,3

  • 1Department of Genetics, Stanford University, Stanford University, Stanford, California 94305, USA.

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|April 26, 2023
PubMed
Summary
This summary is machine-generated.

We optimized the assay for transposase-accessible chromatin using sequencing (ATAC-seq) for the African turquoise killifish. This method profiles the epigenomic landscape, aiding gene expression prediction and regulatory element identification.

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Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Chromatin accessibility is crucial for understanding gene regulation.
  • Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a key technique for epigenomic profiling.
  • The African turquoise killifish (Nothobranchius furzeri) is a valuable model organism for aging and developmental studies.

Purpose of the Study:

  • To optimize and present a robust ATAC-seq protocol for the African turquoise killifish.
  • To enable genome-wide chromatin accessibility analysis in killifish embryos and tissues.
  • To provide a computational pipeline for ATAC-seq data processing and analysis in this species.

Main Methods:

  • Optimized protocol for preparing isolated nuclei from killifish embryos and tissues.
  • Adaptation of ATAC-seq for low-input samples.
  • Next-generation sequencing for high-resolution chromatin accessibility mapping.
  • Development of a bioinformatic pipeline for data analysis.

Main Results:

  • Successfully established an optimized ATAC-seq protocol for Nothobranchius furzeri.
  • Demonstrated the feasibility of profiling epigenomic landscapes from limited biological material.
  • Generated high-quality chromatin accessibility data from killifish samples.
  • Provided a comprehensive pipeline for analyzing ATAC-seq data.

Conclusions:

  • The optimized ATAC-seq protocol facilitates detailed epigenomic studies in the African turquoise killifish.
  • This methodology aids in identifying regulatory elements and predicting gene expression patterns.
  • The provided pipeline supports efficient analysis of killifish ATAC-seq data, advancing research in this model organism.