The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.

The sequencing depth necessary for documenting differential gene expression using RNA-Seq has been little explored outside of model systems. In particular, the depth required to analyze large-scale patterns of differential transcription factor expression is not known. The goal of the present study i...

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Autores principales:	Joel Atallah, David C Plachetzki, W Cameron Jasper, Brian R Johnson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7293e71310374c8b8b97b9d6f3977ee1
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spelling	oai:doaj.org-article:7293e71310374c8b8b97b9d6f3977ee12021-11-18T08:41:41ZThe utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.1932-620310.1371/journal.pone.0084160https://doaj.org/article/7293e71310374c8b8b97b9d6f3977ee12013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24358338/?tool=EBIhttps://doaj.org/toc/1932-6203The sequencing depth necessary for documenting differential gene expression using RNA-Seq has been little explored outside of model systems. In particular, the depth required to analyze large-scale patterns of differential transcription factor expression is not known. The goal of the present study is to explore the effectiveness of shallow (relatively low read depth) RNA-Seq. We focus on two tissues in the honey bee: the sting gland and the digestive tract. The sting gland is an experimentally well-understood tissue that we use to benchmark the utility of this approach. We use the digestive tract to test the results obtained with the sting gland, and to conduct RNA-Seq between tissue types. Using a list of experimentally verified genes conferring tissue-specific functions in the sting gland, we show that relatively little read depth is necessary to identify them. We argue that this result should be broadly applicable, since genes important for tissue-specific functions often have robust expression patterns, and because we obtained similar results in our analysis of the digestive tract. Furthermore, we demonstrate that the differential expression of transcription factors, which are transcribed at low levels compared to other genes, can nevertheless often be determined using shallow RNA-Seq. Overall, we find over 150 differentially expressed transcription factors in our tissues at a read depth of only 12 million. This work shows the utility of low-depth sequencing for identifying genes important for tissue-specific functions. It also verifies the often-held belief that transcription factors show low levels of expression, while demonstrating that, in spite of this, they are frequently amenable to shallow RNA-Seq. Our findings should be of benefit to researchers using RNA-Seq in many different biological systems.Joel AtallahDavid C PlachetzkiW Cameron JasperBrian R JohnsonPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 12, p e84160 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Joel Atallah David C Plachetzki W Cameron Jasper Brian R Johnson The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
description	The sequencing depth necessary for documenting differential gene expression using RNA-Seq has been little explored outside of model systems. In particular, the depth required to analyze large-scale patterns of differential transcription factor expression is not known. The goal of the present study is to explore the effectiveness of shallow (relatively low read depth) RNA-Seq. We focus on two tissues in the honey bee: the sting gland and the digestive tract. The sting gland is an experimentally well-understood tissue that we use to benchmark the utility of this approach. We use the digestive tract to test the results obtained with the sting gland, and to conduct RNA-Seq between tissue types. Using a list of experimentally verified genes conferring tissue-specific functions in the sting gland, we show that relatively little read depth is necessary to identify them. We argue that this result should be broadly applicable, since genes important for tissue-specific functions often have robust expression patterns, and because we obtained similar results in our analysis of the digestive tract. Furthermore, we demonstrate that the differential expression of transcription factors, which are transcribed at low levels compared to other genes, can nevertheless often be determined using shallow RNA-Seq. Overall, we find over 150 differentially expressed transcription factors in our tissues at a read depth of only 12 million. This work shows the utility of low-depth sequencing for identifying genes important for tissue-specific functions. It also verifies the often-held belief that transcription factors show low levels of expression, while demonstrating that, in spite of this, they are frequently amenable to shallow RNA-Seq. Our findings should be of benefit to researchers using RNA-Seq in many different biological systems.
format	article
author	Joel Atallah David C Plachetzki W Cameron Jasper Brian R Johnson
author_facet	Joel Atallah David C Plachetzki W Cameron Jasper Brian R Johnson
author_sort	Joel Atallah
title	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
title_short	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
title_full	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
title_fullStr	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
title_full_unstemmed	The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.
title_sort	utility of shallow rna-seq for documenting differential gene expression in genes with high and low levels of expression.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7293e71310374c8b8b97b9d6f3977ee1
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The utility of shallow RNA-Seq for documenting differential gene expression in genes with high and low levels of expression.

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