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A method for generating highly multiplexed ChIP-seq libraries
BACKGROUND: The barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048252/ https://www.ncbi.nlm.nih.gov/pubmed/24885602 http://dx.doi.org/10.1186/1756-0500-7-312 |
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author | Ford, Ethan Nikopoulou, Chrysa Kokkalis, Antonis Thanos, Dimitris |
author_facet | Ford, Ethan Nikopoulou, Chrysa Kokkalis, Antonis Thanos, Dimitris |
author_sort | Ford, Ethan |
collection | PubMed |
description | BACKGROUND: The barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations and/or technical barriers in their implementation for ChIP-sequencing. FINDINGS: Converting Y-shaped sequencing adapters to double stranded DNA prior to agarose gel size selection reduces adapter dimer contamination and quantitating the number of cycles required for amplification of the library with qPCR prior to library amplification eliminates library over-amplification. CONCLUSIONS: We describe an efficient and cost effective method for making barcoded ChIP-seq libraries for sequencing on the Illumina platform. |
format | Online Article Text |
id | pubmed-4048252 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40482522014-06-07 A method for generating highly multiplexed ChIP-seq libraries Ford, Ethan Nikopoulou, Chrysa Kokkalis, Antonis Thanos, Dimitris BMC Res Notes Technical Note BACKGROUND: The barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations and/or technical barriers in their implementation for ChIP-sequencing. FINDINGS: Converting Y-shaped sequencing adapters to double stranded DNA prior to agarose gel size selection reduces adapter dimer contamination and quantitating the number of cycles required for amplification of the library with qPCR prior to library amplification eliminates library over-amplification. CONCLUSIONS: We describe an efficient and cost effective method for making barcoded ChIP-seq libraries for sequencing on the Illumina platform. BioMed Central 2014-05-22 /pmc/articles/PMC4048252/ /pubmed/24885602 http://dx.doi.org/10.1186/1756-0500-7-312 Text en Copyright © 2014 Ford et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 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 Ford, Ethan Nikopoulou, Chrysa Kokkalis, Antonis Thanos, Dimitris A method for generating highly multiplexed ChIP-seq libraries |
title | A method for generating highly multiplexed ChIP-seq libraries |
title_full | A method for generating highly multiplexed ChIP-seq libraries |
title_fullStr | A method for generating highly multiplexed ChIP-seq libraries |
title_full_unstemmed | A method for generating highly multiplexed ChIP-seq libraries |
title_short | A method for generating highly multiplexed ChIP-seq libraries |
title_sort | method for generating highly multiplexed chip-seq libraries |
topic | Technical Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4048252/ https://www.ncbi.nlm.nih.gov/pubmed/24885602 http://dx.doi.org/10.1186/1756-0500-7-312 |
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