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New methods for next generation sequencing based microRNA expression profiling
BACKGROUND: MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022920/ https://www.ncbi.nlm.nih.gov/pubmed/21171994 http://dx.doi.org/10.1186/1471-2164-11-716 |
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author | Buermans, Henk PJ Ariyurek, Yavuz van Ommen, Gertjan den Dunnen, Johan T 't Hoen, Peter AC |
author_facet | Buermans, Henk PJ Ariyurek, Yavuz van Ommen, Gertjan den Dunnen, Johan T 't Hoen, Peter AC |
author_sort | Buermans, Henk PJ |
collection | PubMed |
description | BACKGROUND: MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer. RESULTS: High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. The sample preparation and E-miR pipeline were used to identify 37 cardiac enriched microRNAs in stage 16 chicken embryos. Isomir expression profiles between the heart and embryo were highly correlated for all miRNAs suggesting that tissue or cell specific miRNA modifications do not occur. CONCLUSIONS: In conclusion, our alternative sample preparation method can successfully be applied to generate high quality miRNA sequencing libraries for the Illumina genome analyzer. |
format | Text |
id | pubmed-3022920 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30229202011-01-19 New methods for next generation sequencing based microRNA expression profiling Buermans, Henk PJ Ariyurek, Yavuz van Ommen, Gertjan den Dunnen, Johan T 't Hoen, Peter AC BMC Genomics Methodology Article BACKGROUND: MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer. RESULTS: High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. The sample preparation and E-miR pipeline were used to identify 37 cardiac enriched microRNAs in stage 16 chicken embryos. Isomir expression profiles between the heart and embryo were highly correlated for all miRNAs suggesting that tissue or cell specific miRNA modifications do not occur. CONCLUSIONS: In conclusion, our alternative sample preparation method can successfully be applied to generate high quality miRNA sequencing libraries for the Illumina genome analyzer. BioMed Central 2010-12-20 /pmc/articles/PMC3022920/ /pubmed/21171994 http://dx.doi.org/10.1186/1471-2164-11-716 Text en Copyright ©2010 Buermans et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Buermans, Henk PJ Ariyurek, Yavuz van Ommen, Gertjan den Dunnen, Johan T 't Hoen, Peter AC New methods for next generation sequencing based microRNA expression profiling |
title | New methods for next generation sequencing based microRNA expression profiling |
title_full | New methods for next generation sequencing based microRNA expression profiling |
title_fullStr | New methods for next generation sequencing based microRNA expression profiling |
title_full_unstemmed | New methods for next generation sequencing based microRNA expression profiling |
title_short | New methods for next generation sequencing based microRNA expression profiling |
title_sort | new methods for next generation sequencing based microrna expression profiling |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3022920/ https://www.ncbi.nlm.nih.gov/pubmed/21171994 http://dx.doi.org/10.1186/1471-2164-11-716 |
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