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Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing

Aptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS...

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Autores principales: Pleiko, Karlis, Saulite, Liga, Parfejevs, Vadims, Miculis, Karlis, Vjaters, Egils, Riekstina, Una
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544647/
https://www.ncbi.nlm.nih.gov/pubmed/31148584
http://dx.doi.org/10.1038/s41598-019-44654-w
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author Pleiko, Karlis
Saulite, Liga
Parfejevs, Vadims
Miculis, Karlis
Vjaters, Egils
Riekstina, Una
author_facet Pleiko, Karlis
Saulite, Liga
Parfejevs, Vadims
Miculis, Karlis
Vjaters, Egils
Riekstina, Una
author_sort Pleiko, Karlis
collection PubMed
description Aptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live cells. Here, we present a differential binding cell-SELEX (systematic evolution of ligands by exponential enrichment) workflow that adapts the FASTAptamer toolbox and bioinformatics tool edgeR, which are primarily used for functional genomics, to achieve more informative metrics about the selection process. We propose a fast and practical high-throughput aptamer identification method to be used with the cell-SELEX technique to increase the aptamer selection rate against live cells. The feasibility of our approach is demonstrated by performing aptamer selection against a clear cell renal cell carcinoma (ccRCC) RCC-MF cell line using the RC-124 cell line from healthy kidney tissue for negative selection.
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spelling pubmed-65446472019-06-09 Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing Pleiko, Karlis Saulite, Liga Parfejevs, Vadims Miculis, Karlis Vjaters, Egils Riekstina, Una Sci Rep Article Aptamers have in recent years emerged as a viable alternative to antibodies. High-throughput sequencing (HTS) has revolutionized aptamer research by increasing the number of reads from a few (using Sanger sequencing) to millions (using an HTS approach). Despite the availability and advantages of HTS compared to Sanger sequencing, there are only 50 aptamer HTS sequencing samples available on public databases. HTS data in aptamer research are primarily used to compare sequence enrichment between subsequent selection cycles. This approach does not take full advantage of HTS because the enrichment of sequences during selection can be due to inefficient negative selection when using live cells. Here, we present a differential binding cell-SELEX (systematic evolution of ligands by exponential enrichment) workflow that adapts the FASTAptamer toolbox and bioinformatics tool edgeR, which are primarily used for functional genomics, to achieve more informative metrics about the selection process. We propose a fast and practical high-throughput aptamer identification method to be used with the cell-SELEX technique to increase the aptamer selection rate against live cells. The feasibility of our approach is demonstrated by performing aptamer selection against a clear cell renal cell carcinoma (ccRCC) RCC-MF cell line using the RC-124 cell line from healthy kidney tissue for negative selection. Nature Publishing Group UK 2019-05-31 /pmc/articles/PMC6544647/ /pubmed/31148584 http://dx.doi.org/10.1038/s41598-019-44654-w Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Pleiko, Karlis
Saulite, Liga
Parfejevs, Vadims
Miculis, Karlis
Vjaters, Egils
Riekstina, Una
Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title_full Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title_fullStr Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title_full_unstemmed Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title_short Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing
title_sort differential binding cell-selex method to identify cell-specific aptamers using high-throughput sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544647/
https://www.ncbi.nlm.nih.gov/pubmed/31148584
http://dx.doi.org/10.1038/s41598-019-44654-w
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