ArticleBMC genomics2018
SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Whole-genome methylation profiling of extracellular vesicle DNA in gastric cancer identifies intercellular communication features.Nature communications · 2025Article
- Chromatin accessibility derived from cfDNA serves as a novel classification biomarker of glioma.Frontiers in oncology · 2025Article
- RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution.Nature communications · 2024Article
- Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.Nucleic acids research · 2024Article
- Telomere-related DNA damage response pathways in cancer therapy: prospective targets.Frontiers in pharmacology · 2024Review
- ArrayedbioRxiv : the preprint server for biology · 2023Article
- A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells.Adipocyte · 2022Article
- Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0.BMC biology · 2022Article
- Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy.Current issues in molecular biology · 2022Review
- Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis.Diagnostics (Basel, Switzerland) · 2021Review
- Adaptor Template Oligo-Mediated Sequencing (ATOM-Seq) is a new ultra-sensitive UMI-based NGS library preparation technology for use with cfDNA and cfRNA.Scientific reports · 2021Article
- The Detection of Cancer Epigenetic Traces in Cell-Free DNA.Frontiers in oncology · 2021Review
- Tn5 Transposase Applied in Genomics Research.International journal of molecular sciences · 2020Review
- A low-bias and sensitive small RNA library preparation method using randomized splint ligation.Nucleic acids research · 2020Article
- Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA.Nature protocols · 2020Article
- Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning.Computational and structural biotechnology journal · 2020Article
- A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos.BMC genomics · 2019Article
- Correction to: SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states.BMC genomics · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
backgroundNext-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings.
resultsThis study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 10
conclusionsThis study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.