Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
AI Summary:
FISHtoFigure is a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data.AI Topics:
Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming 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 computational image analysis 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 in the expression of Cd4 by 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 with Trypanosoma 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.
Bentley-Abbot, Calum
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listHeslop, Rhiannon
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listPirillo, Chiara
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listChandrasegaran, Praveena
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listMcConnell, Gail
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listRoberts, Ed
Author
Hargrave, Kerrie E. and Worrell, Julie C. and Pirillo, Chiara and Brennan, Euan and Masdefiol Garriga, Andreu and Gray, Joshua I. and Purnell, Thomas and Roberts, Edward W. and MacLeod, Megan K.L. (2024) Lung influenza virus specific memory CD4 T cell location and optimal cytokine production are dependent on interactions with lung antigen-presenting cells. Mucosal Immunology, 17 (5). pp. 843-857. ISSN 1933-0219
Kumar, Saumya and Basto, Afonso P. and Ribeiro, Filipa and Almeida, Silvia C.P. and Campos, Patricia and Peres, Carina and Pulvirenti, Nadia and Al-Khalidi, Sarwah and Kilbey, Anna and Tosello, Jimena and Piaggio, Eliane and Russo, Momtchilo and Gama-Carvalho, Margarida and Coffelt, Seth B. and Roberts, Ed W. and Geginat, Jens and Florindo, Helena F. and Graca, Luis (2024) Specialized Tfh cell subsets driving type-1 and type-21 humoral responses in lymphoid tissue. Cell Discovery, 10: 64. ISSN 2056-5968
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listHutchinson, Edward
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listMacLeod, Annette
Author
Bentley-Abbot, Calum and Heslop, Rhiannon and Pirillo, Chiara and Chandrasegaran, Praveena and McConnell, Gail and Roberts, Ed and Hutchinson, Edward and MacLeod, Annette (2024) An easy to use tool for the analysis of subcellular mRNA transcript colocalisation in smFISH data. Scientific Reports, 14: 8348. ISSN 2045-2322
See full publications listAvailable under License Creative Commons Attribution.
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