美国华盛顿大学Brian J. Beliveau研究团队开发出新方法，实现寡核苷酸FISH实验的交互式设计。相关论文于2021年7月5日在线发表于国际学术期刊《自然—方法学》。

研究人员表示，荧光原位杂交（FISH）使研究人员能够可视化固定样本中核酸的空间位置和数量。最近，在开发基于寡核苷酸（oligo）的FISH方法方面取得了相当大的进展，使科研人员能够以超分辨率研究基因组的三维组织，并可视化单个细胞中数千个基因的基因表达空间模式。然而，很少有现有的计算工具可以支持使用寡聚FISH探针进行这些实验所需的生物信息学工作流程。

研究人员开发了PaintSHOP（paint server and homology optimization pipeline），这是一个用于设计寡聚FISH实验的交互式平台。PaintSHOP使研究人员能够有效地识别其实验目标的探针，合并其他必要的序列，例如引物对，并轻松生成记录文库设计的文件。PaintSHOP使得复杂探针组的设计更为简便和标准化。

附：英文原文

Title: PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments

Author: Elliot A. Hershberg, Conor K. Camplisson, Jennie L. Close, Sahar Attar, Ryan Chern, Yuzhen Liu, Shreeram Akilesh, Philip R. Nicovich, Brian J. Beliveau

Issue&Volume: 2021-07-05

Abstract: Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments using oligo FISH probes. Here, we introduce paint server and homology optimization pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs and to easily generate files documenting library design. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community. Paint server and homology optimization pipeline (PaintSHOP), an interactive platform for the design of oligo fluorescence in situ hybridization (FISH) experiments, democratizes and standardizes the process of designing complex probe sets for the oligo FISH community.

DOI: 10.1038/s41592-021-01187-3

Source: https://www.nature.com/articles/s41592-021-01187-3