FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data
FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data
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FISHtoFigure：一种易于使用的工具，用于快速、多目标分区和分析 smFISH 数据中的亚细胞 mRNA 转录本
DOI：
10.1101/2023.06.28.546871
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Bentley-Abbot C
中科院分区：
文献类型：
--
作者：
Bentley-Abbot C
单分子荧光原位杂交(SmFISH)已成为研究单细胞mRNA表达的有价值的工具。然而，使用目前可用的开源分析软件包提取和分析有关转录本表达的定量数据需要相当数量的生物信息学专业知识。在这里，我们介绍FISHtoFigure，这是一个专门为分析QuPath量化的、多标记的smFISH数据中的mRNA丰度和共表达而开发的新软件工具。FISHtoFigure有助于对感兴趣的转录本进行自动空间分析，允许用户分析对特定的信使核糖核酸靶标组合呈阳性的细胞群体，而不需要生物信息学专业知识。作为概念验证和展示这一新研究工具的能力，我们在多个生物系统中验证了FISHtoFigure。我们使用FISHtoFigure鉴定了感染甲型流感病毒的小鼠脾中T细胞的上调，然后分析了更复杂的数据，显示感染布氏锥虫的小鼠大脑中小胶质细胞和调节B细胞之间存在串扰。这些分析证明了使用FISHtoFigure分析细胞表达谱是多么容易，以及这一新工具在smFISH数据分析领域的价值。
Single molecule fluorescencein situhybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of bioinformatic expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for bioinformatics expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation of T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected withTrypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.
影响因子：
4.1
作者：
Wang, Fay;Flanagan, John;Luo, Yuling
通讯作者：
Luo, Yuling
影响因子：
14.9
作者：
K. Maynard;M. Tippani;Y. Takahashi;BaDoi N. Phan;T. Hyde;A. Jaffe;K. Martinowich
通讯作者：
K. Maynard;M. Tippani;Y. Takahashi;BaDoi N. Phan;T. Hyde;A. Jaffe;K. Martinowich
pandas-dev/pandas：Pandas 1.1.3
DOI：
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发表时间：
2020
期刊：
影响因子：
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作者：
Jeff Reback;Wes McKinney;jbrockmendel;Joris Van den Bossche;Tom Augspurger;Phillip Cloud;gfyoung;Sinhrks;Simon Hawkins;Adam Klein;Matthew Roeschke;Jeff Tratner;Terji Petersen;Chang She;William Ayd;MomIsBestFriend;M. García;Jeremy Schendel;Andy Hayden;Daniel Saxton;Vytautas Jancauskas;Ali McMaster;Pietro Battiston;Skipper Seabold;chris;h;Kaiqi Dong;Stephan Hoyer;W. Overmeire;Martin Winkel
通讯作者：
Martin Winkel