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Method for RNA extraction and transcriptomic analysis of single fungal spores

Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian...

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Autores principales: Geoghegan, Ivey A., Emes, Richard D., Archer, David B., Avery, Simon V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938798/
https://www.ncbi.nlm.nih.gov/pubmed/31908984
http://dx.doi.org/10.1016/j.mex.2019.12.002
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author Geoghegan, Ivey A.
Emes, Richard D.
Archer, David B.
Avery, Simon V.
author_facet Geoghegan, Ivey A.
Emes, Richard D.
Archer, David B.
Avery, Simon V.
author_sort Geoghegan, Ivey A.
collection PubMed
description Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian cells, due to their ease of lysis and high RNA content. No single cell transcriptomic analysis has yet been described in microbial spores, even though it is known that heterogeneity at the phenotype level exists among individual spores. Transcriptomic analysis of single spores is challenging, in part due to the physically robust nature of the spore wall. This precludes the use of methods commonly used for mammalian cells. Here, we describe a simple method for extraction and amplification of transcripts from single fungal conidia (asexual spores), and its application in single-cell transcriptomics studies. The method can also be used for studies of small numbers of fungal conidia, which may be necessary in the case of limited sample availability, low-abundance transcripts or interest in small subpopulations of conidia. • The method allows detection of transcripts from single conidia of Aspergillus niger; • The method allows detection of genomic DNA from single conidia of Aspergillus niger.
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spelling pubmed-69387982020-01-06 Method for RNA extraction and transcriptomic analysis of single fungal spores Geoghegan, Ivey A. Emes, Richard D. Archer, David B. Avery, Simon V. MethodsX Biochemistry, Genetics and Molecular Biology Transcriptomic analysis of single cells has been increasingly in demand in recent years, thanks to technological and methodological advances as well as growing recognition of the importance of individuals in biological systems. However, the majority of these studies have been performed in mammalian cells, due to their ease of lysis and high RNA content. No single cell transcriptomic analysis has yet been described in microbial spores, even though it is known that heterogeneity at the phenotype level exists among individual spores. Transcriptomic analysis of single spores is challenging, in part due to the physically robust nature of the spore wall. This precludes the use of methods commonly used for mammalian cells. Here, we describe a simple method for extraction and amplification of transcripts from single fungal conidia (asexual spores), and its application in single-cell transcriptomics studies. The method can also be used for studies of small numbers of fungal conidia, which may be necessary in the case of limited sample availability, low-abundance transcripts or interest in small subpopulations of conidia. • The method allows detection of transcripts from single conidia of Aspergillus niger; • The method allows detection of genomic DNA from single conidia of Aspergillus niger. Elsevier 2019-12-04 /pmc/articles/PMC6938798/ /pubmed/31908984 http://dx.doi.org/10.1016/j.mex.2019.12.002 Text en © 2019 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Biochemistry, Genetics and Molecular Biology
Geoghegan, Ivey A.
Emes, Richard D.
Archer, David B.
Avery, Simon V.
Method for RNA extraction and transcriptomic analysis of single fungal spores
title Method for RNA extraction and transcriptomic analysis of single fungal spores
title_full Method for RNA extraction and transcriptomic analysis of single fungal spores
title_fullStr Method for RNA extraction and transcriptomic analysis of single fungal spores
title_full_unstemmed Method for RNA extraction and transcriptomic analysis of single fungal spores
title_short Method for RNA extraction and transcriptomic analysis of single fungal spores
title_sort method for rna extraction and transcriptomic analysis of single fungal spores
topic Biochemistry, Genetics and Molecular Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6938798/
https://www.ncbi.nlm.nih.gov/pubmed/31908984
http://dx.doi.org/10.1016/j.mex.2019.12.002
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