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Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion
The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample....
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566562/ https://www.ncbi.nlm.nih.gov/pubmed/32759389 http://dx.doi.org/10.1261/rna.076562.120 |
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author | Thompson, Mary Kay Kiourlappou, Maria Davis, Ilan |
author_facet | Thompson, Mary Kay Kiourlappou, Maria Davis, Ilan |
author_sort | Thompson, Mary Kay |
collection | PubMed |
description | The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-min protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable “open source” design strategy would enable virtually any laboratory to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment. |
format | Online Article Text |
id | pubmed-7566562 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-75665622020-11-01 Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion Thompson, Mary Kay Kiourlappou, Maria Davis, Ilan RNA Method The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-min protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable “open source” design strategy would enable virtually any laboratory to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment. Cold Spring Harbor Laboratory Press 2020-11 /pmc/articles/PMC7566562/ /pubmed/32759389 http://dx.doi.org/10.1261/rna.076562.120 Text en © 2020 Thompson et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by/4.0/ This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Method Thompson, Mary Kay Kiourlappou, Maria Davis, Ilan Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title | Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title_full | Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title_fullStr | Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title_full_unstemmed | Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title_short | Ribo-Pop: simple, cost-effective, and widely applicable ribosomal RNA depletion |
title_sort | ribo-pop: simple, cost-effective, and widely applicable ribosomal rna depletion |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566562/ https://www.ncbi.nlm.nih.gov/pubmed/32759389 http://dx.doi.org/10.1261/rna.076562.120 |
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