Xenomake：用于空间转录组实验中异种移植序列处理和排序的管道

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

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BIOINFORMATICS

影响因子:5.4

分区:生物学3区 / 生化研究方法3区生物工程与应用微生物3区数学与计算生物学3区

发表日期:2024 Nov 01

作者: Benjamin S Strope, Katherine E Pendleton, William Z Bowie, Gloria V Echeverria, Qian Zhu

DOI: 10.1093/bioinformatics/btae608

摘要

异种移植模型是模拟人类肿瘤生物学的理想模型，允许干预肿瘤微环境并研究其药物反应。空间分辨转录组学（SRT）为研究异种移植模型的组织结构提供了强有力的工具，但目前缺乏专门的处理来自SRT实验的异种移植序列的管道。Xenomake是一个独立的自动化处理空间异种移植序列的管道，涵盖序列处理、比对、异种移植序列排序等步骤，并与后续的空间分析软件包良好集成。我们还展示了Xenomake能正确分配物种特异性序列，减少数据稀疏性，通过增加基因计数保持生物学相关性。Xenomake为开源项目，可在Github（https://github.com/qianzhulab/Xenomake）获取，完整的文档也可在链接中查阅。

Abstract

Xenograft models are attractive models that mimic human tumor biology and permit one to perturb the tumor microenvironment and study its drug response. Spatially resolved transcriptomics (SRT) provides a powerful way to study the organization of xenograft models, but currently there is a lack of specialized pipeline for processing xenograft reads originated from SRT experiments. Xenomake is a standalone pipeline for the automated handling of spatial xenograft reads. Xenomake handles read processing, alignment, xenograft read sorting, and connects well with downstream spatial analysis packages. We additionally show that Xenomake can correctly assign organism-specific reads, reduce sparsity of data by increasing gene counts, while maintaining biological relevance for studies.Xenomake is an open-source program that is available on Github (https://github.com/qianzhulab/Xenomake). Complete documentation can be found at the link.