TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experiments,STEM CELLS Translational Medicine

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TransSynW: A single‐cell RNA‐sequencing based web application to guide cell conversion experiments
STEM CELLS Translational Medicine ( IF 5.4 ) Pub Date : 2020-10-08 , DOI: 10.1002/sctm.20-0227
Mariana Messias Ribeiro ₁ , Satoshi Okawa _{1,

2} , Antonio Del Sol _{1,

3,

4}

Affiliation

Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single‐cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single‐cell RNA‐sequencing (scRNA‐seq) data and the concomitant increase in the interest expressed by researchers in generating a wide range of functional cells prompted us to develop a computational tool for tackling this challenge. Here we introduce a web application, TransSynW, which uses scRNA‐seq data for predicting cell conversion transcription factors (TFs) for user‐specified cell populations. TransSynW prioritizes pioneer factors among predicted conversion TFs to facilitate chromatin opening often required for cell conversion. In addition, it predicts marker genes for assessing the performance of cell conversion experiments. Furthermore, TransSynW does not require users' knowledge of computer programming and computational resources. We applied TransSynW to different levels of cell conversion specificity, which recapitulated known conversion TFs at each level. We foresee that TransSynW will be a valuable tool for guiding experimentalists to design novel protocols for cell conversion in stem cell research and regenerative medicine.

中文翻译：

TransSynW：基于单细胞 RNA 测序的 Web 应用程序，用于指导细胞转化实验

通过细胞转化产生所需的细胞类型仍然是一个挑战。特别是，由单细胞技术鉴定的新细胞亚型的衍生将为细胞治疗开辟新的策略。最近单细胞 RNA 测序 (scRNA-seq) 数据生成的增加以及研究人员对生成各种功能细胞的兴趣随之增加，这促使我们开发了一种计算工具来应对这一挑战。在这里，我们介绍了一个 Web 应用程序 TransSynW，它使用 scRNA-seq 数据来预测用户指定细胞群的细胞转化转录因子 (TF)。TransSynW 在预测的转化 TF 中优先考虑先驱因子，以促进细胞转化通常需要的染色质开放。此外，它预测用于评估细胞转化实验性能的标记基因。此外，TransSynW 不需要用户具备计算机编程和计算资源的知识。我们将 TransSynW 应用于不同级别的细胞转化特异性，概括了每个级别的已知转化 TF。我们预计 TransSynW 将成为指导实验人员设计干细胞研究和再生医学中细胞转化新方案的宝贵工具。

更新日期：2020-10-08

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