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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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SEAseq: a portable and cloud-based chromatin occupancy analysis suite.

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  • 1Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

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SEAseq is a new computational pipeline for analyzing Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing data. It offers a user-friendly, cloud-based solution for complex genomic analyses, overcoming computational resource limitations.

Keywords:
Analysis pipelineCUT&RUNChIP sequencingCloudComputational genomicsData analysisGEOMotif analysisPeak callingPlatform independentSRA

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide protein-DNA binding is typically studied using Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing.
  • These methods generate large datasets requiring sophisticated, computationally intensive tools, posing a barrier to researchers with limited computational resources.

Purpose of the Study:

  • To develop a comprehensive, infrastructure-independent computational pipeline for processing and analyzing ChIP-Seq and CUT&RUN data.
  • To provide a user-friendly and accessible tool for genomic data analysis, regardless of programming skills or available computational resources.

Main Methods:

  • Developed SEAseq, a computational pipeline leveraging open-source tools for ChIP-Seq/CUT&RUN data analysis.
  • SEAseq integrates alignment, peak calling, motif analysis, coverage profiling, peak annotation, super-enhancer identification, and quality assessment.
  • The pipeline offers cloud implementation and local installation options.

Main Results:

  • SEAseq performs extensive analyses from raw experimental output, including advanced genomic feature identification.
  • The pipeline facilitates rapid and cost-effective analysis of both new and existing datasets.
  • Comparative case studies demonstrated the pipeline's effectiveness.

Conclusions:

  • SEAseq provides an easy-to-use, versatile, reliable, and efficient resource for high-quality ChIP-Seq and CUT&RUN data analysis.
  • Its cloud implementation makes advanced analyses accessible even with constrained computational resources.
  • SEAseq is platform-independent and designed for universal usability.