ArticleScientific reports2019
Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Selection of aptamers against triple negative breast cancer cells using high throughput sequencing.Scientific reports · 2021Trial
- Selection and validation of novel DNA aptamer panel co-specific toMolecular therapy. Nucleic acids · 2026Article
- Review
- ASSET: A Framework for Decoding Aptamer Specificity of an Enriched Library by Next-Generation Sequencing of Experimental Samples.bioRxiv : the preprint server for biology · 2025Article
- Targeting triple-negative breast cancer cells with a β1-integrin binding aptamer.Molecular therapy. Nucleic acids · 2023Article
- A Rapid and Sensitive Aptamer-Based Biosensor for Amnesic Shellfish Toxin Domoic Acid.Bioengineering (Basel, Switzerland) · 2022Article
- Development and characterization of DNA aptamer against Retinoblastoma by Cell-SELEX.Scientific reports · 2022Article
- Identification of G-quadruplex anti-Interleukin-2 aptamer with high specificity through SELEX stringency.Heliyon · 2022Article
- Profiling Cancer Cells by Cell-SELEX: Use of Aptamers for Discovery of Actionable Biomarkers and Therapeutic Applications Thereof.Pharmaceutics · 2021Review
- Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders.International journal of molecular sciences · 2021Review
- Novel Approach to Overcome Defects of Cell-SELEX in Developing Aptamers against Aspartate β-Hydroxylase.ACS omega · 2021Article
- Recent Advances in Nanomaterial-Based Aptasensors in Medical Diagnosis and Therapy.Nanomaterials (Basel, Switzerland) · 2021Review
- Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology.International journal of molecular sciences · 2020Review
- CRISPR-Mediated Isogenic Cell-SELEX Approach for Generating Highly Specific Aptamers Against Native Membrane Proteins.Cellular and molecular bioengineering · 2020Article
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Authors and funding
6 authors.
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Abstract
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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