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Related Experiment Video

Updated: Jun 10, 2025

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
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Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments.

Benjamin S Strope1,2, Katherine E Pendleton1,2,3, William Z Bowie1,2

  • 1Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, United States.

Bioinformatics (Oxford, England)
|October 14, 2024
PubMed
Summary

Xenomake is a new bioinformatics pipeline that automates spatial xenograft data processing. This tool enhances gene counts and maintains biological relevance for improved tumor microenvironment studies.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Cancer Research

Background:

  • Xenograft models are crucial for studying human tumor biology and drug responses.
  • Spatially resolved transcriptomics (SRT) offers insights into xenograft model organization.
  • A specialized pipeline for SRT xenograft data processing is currently lacking.

Purpose of the Study:

  • To develop Xenomake, a standalone pipeline for automated processing of spatial xenograft reads.
  • To facilitate downstream spatial analysis of xenograft data.

Main Methods:

  • Xenomake automates read processing, alignment, and xenograft read sorting.
  • The pipeline is designed for seamless integration with existing spatial analysis packages.

Main Results:

  • Xenomake correctly assigns organism-specific reads.
  • The pipeline reduces data sparsity by increasing gene counts.
  • Biological relevance is maintained throughout the data processing.

Conclusions:

  • Xenomake addresses the need for specialized xenograft SRT data processing.
  • The pipeline enhances data quality and supports critical tumor microenvironment research.