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<p>In this Resource, we present an extensive dataset of chemical-induced gene signatures (CIGS), encompassing expression patterns of 3,407 genes regulating key biological processes in 2 human cell lines exposed to 13,221 compounds across 93,664 perturbations. This dataset encompasses 319,045,108 gene expression events, generated through 2 high-throughput technologies: the previously documented high-throughput sequencing-based high-throughput screening (HTS<sup>2</sup>) and the newly developed highly multiplexed and parallel sequencing (HiMAP-seq). Our results show that HiMAP-seq is comparable to RNA sequencing, but can profile the expression of thousands of genes across thousands of samples in one single test by utilizing a pooled-sample strategy. We further illustrate CIGS’s utility in elucidating the mechanism of action of unannotated small molecules, like ligustroflavone and 2,4-dihydroxybenzaldehyde, and to identify perturbation-induced cell states, such as those resistant to ferroptosis. The full dataset is publicly accessible at <a href="https://cigs.iomicscloud.com/">https://cigs.iomicscloud.com/</a>.</p>

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High-throughput profiling of chemical-induced gene expression across 93,644 perturbations

  • 期刊论文

  • 发表日期：

    2025年8月18日

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  • Lei Xiang,
  • Yumei Wang,
  • Wei Shao,
  • Qingzhou Li,
  • Xiankuo Yu,
  • Mingming Wei,
  • Yu Gui,
  • Shengrong Li,
  • Pan Qin,
  • Chao Hu,
  • Guochen Zhang,
  • Xianwen Zhang,
  • Jiawen Wang,
  • Yingying Li,
  • Jun An,
  • Yan Luo,
  • Yile Liao,
  • Jinghong Deng,
  • Xinran Tai,
  • Richard Y. Xu,
  • Lijun Huang,
  • Dale Guo,
  • Guanbin Zhang,
  • Zhi Xie,
  • Yun Deng,
  • Junquan Xu,
  • Dong Wang

摘要

In this Resource, we present an extensive dataset of chemical-induced gene signatures (CIGS), encompassing expression patterns of 3,407 genes regulating key biological processes in 2 human cell lines exposed to 13,221 compounds across 93,664 perturbations. This dataset encompasses 319,045,108 gene expression events, generated through 2 high-throughput technologies: the previously documented high-throughput sequencing-based high-throughput screening (HTS2) and the newly developed highly multiplexed and parallel sequencing (HiMAP-seq). Our results show that HiMAP-seq is comparable to RNA sequencing, but can profile the expression of thousands of genes across thousands of samples in one single test by utilizing a pooled-sample strategy. We further illustrate CIGS’s utility in elucidating the mechanism of action of unannotated small molecules, like ligustroflavone and 2,4-dihydroxybenzaldehyde, and to identify perturbation-induced cell states, such as those resistant to ferroptosis. The full dataset is publicly accessible at https://cigs.iomicscloud.com/.