Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA
Next generation RNA-sequencing (RNA-seq) is a flexible approach that can be applied to a range of applications including global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and profiling of expressed mutations. Many RNA-seq protocols requir...
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| Veröffentlicht in: | PloS one 2019-10, Vol.14 (10), p.e0224578 |
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| creator | Haile, Simon Corbett, Richard D Bilobram, Steve Mungall, Karen Grande, Bruno M Kirk, Heather Pandoh, Pawan MacLeod, Tina McDonald, Helen Bala, Miruna Coope, Robin J Moore, Richard A Mungall, Andrew J Zhao, Yongjun Morin, Ryan D Jones, Steven J Marra, Marco A |
| description | Next generation RNA-sequencing (RNA-seq) is a flexible approach that can be applied to a range of applications including global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and profiling of expressed mutations. Many RNA-seq protocols require up to microgram levels of total RNA input amounts to generate high quality data, and thus remain impractical for the limited starting material amounts typically obtained from rare cell populations, such as those from early developmental stages or from laser micro-dissected clinical samples. Here, we present an assessment of the contemporary ribosomal RNA depletion-based protocols, and identify those that are suitable for inputs as low as 1-10 ng of intact total RNA and 100-500 ng of partially degraded RNA from formalin-fixed paraffin-embedded tissues. |
| doi_str_mv | 10.1371/journal.pone.0224578 |
| format | Article |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Base Sequence - genetics Biochemistry Bioinformatics Biology and life sciences Cancer Consortia Criminal investigation Depletion Developmental stages Formaldehyde Gene expression Gene Expression Profiling - methods Gene sequencing Genomes Genomics High-Throughput Nucleotide Sequencing - methods Humans Lymphoma Mammals Mammals - genetics Methods Molecular biology Mutation Paraffin Paraffins Protocol Research and analysis methods Ribosomal RNA RNA RNA - genetics RNA sequencing RNA, Messenger - genetics RNA, Ribosomal - genetics rRNA Sequence Analysis, RNA - methods Splicing Structural analysis Tissue Fixation - methods Transcription Transcriptome - genetics |
| title | Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA |
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