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Related Experiment Video

Updated: Jul 16, 2025

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Published on: February 26, 2015

Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments.

Benjamin S Strope^1,2, Katherine E Pendleton^1,2,3, William Z Bowie^1,2

¹Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.

Biorxiv : the Preprint Server for Biology

|September 21, 2023

Summary

Xenomake is a new pipeline for processing spatial xenograft data. It automates analysis, improves gene counts, and maintains biological relevance for tumor microenvironment studies.

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Area of Science:

Oncology
Genomics
Bioinformatics

Background:

Xenograft models are crucial for studying human tumor biology and drug responses within the tumor microenvironment.
Spatially resolved transcriptomics (SRT) offers powerful insights into xenograft model organization.
A specialized bioinformatics pipeline is lacking for processing SRT data from xenografts.

Approach:

Developed Xenomake, a standalone, automated pipeline for handling spatial xenograft reads.
Xenomake integrates read processing, alignment, xenograft read sorting, and quantification.
The pipeline seamlessly connects with downstream spatial analysis packages.

Key Points:

Xenomake effectively assigns organism-specific reads in mixed xenograft samples.
The pipeline reduces data sparsity by increasing gene counts.
Xenomake maintains the biological relevance of the data for downstream studies.

Conclusions:

Xenomake provides an automated solution for analyzing SRT data in xenograft models.
This pipeline enhances data quality and facilitates deeper biological insights.
Xenomake supports comprehensive studies of the tumor microenvironment and drug responses.