Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response

Abstract Single-cell RNA-seq is a powerful tool for revealing heterogeneity in cancer cells. However, each of the current single-cell RNA-seq platforms has inherent advantages and disadvantages. Here, we show that combining the different single-cell RNA-seq platforms can be an effective approach to...

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Autores principales:	Yukie Kashima, Ayako Suzuki, Ying Liu, Masahito Hosokawa, Hiroko Matsunaga, Masataka Shirai, Kohji Arikawa, Sumio Sugano, Takashi Kohno, Haruko Takeyama, Katsuya Tsuchihara, Yutaka Suzuki
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8f48ed8258fd4e5399c4358ae8f1ca6e
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spelling	oai:doaj.org-article:8f48ed8258fd4e5399c4358ae8f1ca6e2021-12-02T16:08:13ZCombinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response10.1038/s41598-018-21161-y2045-2322https://doaj.org/article/8f48ed8258fd4e5399c4358ae8f1ca6e2018-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-21161-yhttps://doaj.org/toc/2045-2322Abstract Single-cell RNA-seq is a powerful tool for revealing heterogeneity in cancer cells. However, each of the current single-cell RNA-seq platforms has inherent advantages and disadvantages. Here, we show that combining the different single-cell RNA-seq platforms can be an effective approach to obtaining complete information about expression differences and a sufficient cellular population to understand transcriptional heterogeneity in cancers. We demonstrate that it is possible to estimate missing expression information. We further demonstrate that even in the cases where precise information for an individual gene cannot be inferred, the activity of given transcriptional modules can be analyzed. Interestingly, we found that two distinct transcriptional modules, one associated with the Aurora kinase gene and the other with the DUSP gene, are aberrantly regulated in a minor population of cells and may thus contribute to the possible emergence of dormancy or eventual drug resistance within the population.Yukie KashimaAyako SuzukiYing LiuMasahito HosokawaHiroko MatsunagaMasataka ShiraiKohji ArikawaSumio SuganoTakashi KohnoHaruko TakeyamaKatsuya TsuchiharaYutaka SuzukiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-16 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yukie Kashima Ayako Suzuki Ying Liu Masahito Hosokawa Hiroko Matsunaga Masataka Shirai Kohji Arikawa Sumio Sugano Takashi Kohno Haruko Takeyama Katsuya Tsuchihara Yutaka Suzuki Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
description	Abstract Single-cell RNA-seq is a powerful tool for revealing heterogeneity in cancer cells. However, each of the current single-cell RNA-seq platforms has inherent advantages and disadvantages. Here, we show that combining the different single-cell RNA-seq platforms can be an effective approach to obtaining complete information about expression differences and a sufficient cellular population to understand transcriptional heterogeneity in cancers. We demonstrate that it is possible to estimate missing expression information. We further demonstrate that even in the cases where precise information for an individual gene cannot be inferred, the activity of given transcriptional modules can be analyzed. Interestingly, we found that two distinct transcriptional modules, one associated with the Aurora kinase gene and the other with the DUSP gene, are aberrantly regulated in a minor population of cells and may thus contribute to the possible emergence of dormancy or eventual drug resistance within the population.
format	article
author	Yukie Kashima Ayako Suzuki Ying Liu Masahito Hosokawa Hiroko Matsunaga Masataka Shirai Kohji Arikawa Sumio Sugano Takashi Kohno Haruko Takeyama Katsuya Tsuchihara Yutaka Suzuki
author_facet	Yukie Kashima Ayako Suzuki Ying Liu Masahito Hosokawa Hiroko Matsunaga Masataka Shirai Kohji Arikawa Sumio Sugano Takashi Kohno Haruko Takeyama Katsuya Tsuchihara Yutaka Suzuki
author_sort	Yukie Kashima
title	Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
title_short	Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
title_full	Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
title_fullStr	Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
title_full_unstemmed	Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response
title_sort	combinatory use of distinct single-cell rna-seq analytical platforms reveals the heterogeneous transcriptome response
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/8f48ed8258fd4e5399c4358ae8f1ca6e
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Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response

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