Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment

Abstract To better understand the full-length transcriptome of the nucleus accumbens (NAc)—a key brain reward region—in chronic cocaine treatment, we perform the first single molecule, long-read sequencing analysis using the Iso-seq method to detect 42,114 unique transcripts from mouse NAc polyadeny...

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Autores principales:	Molly Estill, Efrain Ribeiro, Nancy J. Francoeur, Melissa L. Smith, Robert Sebra, Szu-Ying Yeh, Ashley M. Cunningham, Eric J. Nestler, Li Shen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/63fe549b0c524dd38ff824a5f1b22884
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spelling	oai:doaj.org-article:63fe549b0c524dd38ff824a5f1b228842021-12-02T11:45:01ZLong read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment10.1038/s41598-021-86068-72045-2322https://doaj.org/article/63fe549b0c524dd38ff824a5f1b228842021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86068-7https://doaj.org/toc/2045-2322Abstract To better understand the full-length transcriptome of the nucleus accumbens (NAc)—a key brain reward region—in chronic cocaine treatment, we perform the first single molecule, long-read sequencing analysis using the Iso-seq method to detect 42,114 unique transcripts from mouse NAc polyadenylated RNA. Using GENCODE annotation as a reference, we find that over half of the Iso-seq derived transcripts are annotated, while 46% of them harbor novel splicing events in known genes; around 1% of them correspond to other types of novel transcripts, such as fusion, antisense and intergenic. Approximately 34% of the novel transcripts are matched with a compiled transcriptome assembled from published short-read data from various tissues, with the remaining 69% being unique to NAc. These data provide a more complete picture of the NAc transcriptome than existing annotations and can serve as a comprehensive reference for future transcriptomic analyses of this important brain reward region.Molly EstillEfrain RibeiroNancy J. FrancoeurMelissa L. SmithRobert SebraSzu-Ying YehAshley M. CunninghamEric J. NestlerLi ShenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Molly Estill Efrain Ribeiro Nancy J. Francoeur Melissa L. Smith Robert Sebra Szu-Ying Yeh Ashley M. Cunningham Eric J. Nestler Li Shen Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
description	Abstract To better understand the full-length transcriptome of the nucleus accumbens (NAc)—a key brain reward region—in chronic cocaine treatment, we perform the first single molecule, long-read sequencing analysis using the Iso-seq method to detect 42,114 unique transcripts from mouse NAc polyadenylated RNA. Using GENCODE annotation as a reference, we find that over half of the Iso-seq derived transcripts are annotated, while 46% of them harbor novel splicing events in known genes; around 1% of them correspond to other types of novel transcripts, such as fusion, antisense and intergenic. Approximately 34% of the novel transcripts are matched with a compiled transcriptome assembled from published short-read data from various tissues, with the remaining 69% being unique to NAc. These data provide a more complete picture of the NAc transcriptome than existing annotations and can serve as a comprehensive reference for future transcriptomic analyses of this important brain reward region.
format	article
author	Molly Estill Efrain Ribeiro Nancy J. Francoeur Melissa L. Smith Robert Sebra Szu-Ying Yeh Ashley M. Cunningham Eric J. Nestler Li Shen
author_facet	Molly Estill Efrain Ribeiro Nancy J. Francoeur Melissa L. Smith Robert Sebra Szu-Ying Yeh Ashley M. Cunningham Eric J. Nestler Li Shen
author_sort	Molly Estill
title	Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
title_short	Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
title_full	Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
title_fullStr	Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
title_full_unstemmed	Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
title_sort	long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/63fe549b0c524dd38ff824a5f1b22884
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Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatment

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