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An automated method for efficient, accurate and reproducible construction of RNA-seq libraries

BACKGROUND: Integration of RNA-seq expression data with knowledge on chromatin accessibility, histone modifications, DNA methylation, and transcription factor binding has been instrumental for the unveiling of cell-specific local and long-range regulatory patterns, facilitating further investigation...

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Autores principales: Tsompana, Maria, Valiyaparambil, Sujith, Bard, Jonathan, Marzullo, Brandon, Nowak, Norma, Buck, Michael Joseph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391147/
https://www.ncbi.nlm.nih.gov/pubmed/25879881
http://dx.doi.org/10.1186/s13104-015-1089-9
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author Tsompana, Maria
Valiyaparambil, Sujith
Bard, Jonathan
Marzullo, Brandon
Nowak, Norma
Buck, Michael Joseph
author_facet Tsompana, Maria
Valiyaparambil, Sujith
Bard, Jonathan
Marzullo, Brandon
Nowak, Norma
Buck, Michael Joseph
author_sort Tsompana, Maria
collection PubMed
description BACKGROUND: Integration of RNA-seq expression data with knowledge on chromatin accessibility, histone modifications, DNA methylation, and transcription factor binding has been instrumental for the unveiling of cell-specific local and long-range regulatory patterns, facilitating further investigation on the underlying rules of transcription regulation at an individual and allele-specific level. However, full genome transcriptome characterization has been partially limited by the complexity and increased time-requirements of available RNA-seq library construction protocols. FINDINGS: Use of the SX-8G IP-Star® Compact System significantly reduces the hands-on time for RNA-seq library synthesis, adenylation, and adaptor ligation providing with high quality RNA-seq libraries tailored for Illumina high-throughput next-generation sequencing. Generated data exhibits high technical reproducibility compared to data from RNA-seq libraries synthesized manually for the same samples. Obtained results are consistent regardless the researcher, day of the experiment, and experimental run. CONCLUSIONS: Overall, the SX-8G IP-Star® Compact System proves an efficient, fast and reliable tool for the construction of next-generation RNA-seq libraries especially for trancriptome-based annotation of larger genomes.
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spelling pubmed-43911472015-04-10 An automated method for efficient, accurate and reproducible construction of RNA-seq libraries Tsompana, Maria Valiyaparambil, Sujith Bard, Jonathan Marzullo, Brandon Nowak, Norma Buck, Michael Joseph BMC Res Notes Technical Note BACKGROUND: Integration of RNA-seq expression data with knowledge on chromatin accessibility, histone modifications, DNA methylation, and transcription factor binding has been instrumental for the unveiling of cell-specific local and long-range regulatory patterns, facilitating further investigation on the underlying rules of transcription regulation at an individual and allele-specific level. However, full genome transcriptome characterization has been partially limited by the complexity and increased time-requirements of available RNA-seq library construction protocols. FINDINGS: Use of the SX-8G IP-Star® Compact System significantly reduces the hands-on time for RNA-seq library synthesis, adenylation, and adaptor ligation providing with high quality RNA-seq libraries tailored for Illumina high-throughput next-generation sequencing. Generated data exhibits high technical reproducibility compared to data from RNA-seq libraries synthesized manually for the same samples. Obtained results are consistent regardless the researcher, day of the experiment, and experimental run. CONCLUSIONS: Overall, the SX-8G IP-Star® Compact System proves an efficient, fast and reliable tool for the construction of next-generation RNA-seq libraries especially for trancriptome-based annotation of larger genomes. BioMed Central 2015-04-03 /pmc/articles/PMC4391147/ /pubmed/25879881 http://dx.doi.org/10.1186/s13104-015-1089-9 Text en © Tsompana et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Technical Note
Tsompana, Maria
Valiyaparambil, Sujith
Bard, Jonathan
Marzullo, Brandon
Nowak, Norma
Buck, Michael Joseph
An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title_full An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title_fullStr An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title_full_unstemmed An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title_short An automated method for efficient, accurate and reproducible construction of RNA-seq libraries
title_sort automated method for efficient, accurate and reproducible construction of rna-seq libraries
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391147/
https://www.ncbi.nlm.nih.gov/pubmed/25879881
http://dx.doi.org/10.1186/s13104-015-1089-9
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