Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Splinted Ligation Adapter Tagging, a novel library preparation for whole genome bisulphite sequencing

ABSTRACT: Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.

ORGANISM(S): Homo sapiens

PROVIDER: GSE89213 | GEO | 2016/10/27

SECONDARY ACCESSION(S): PRJNA350687

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Homo sapiens

Project description:Splinted Ligation Adapter Tagging, a novel library preparation for whole genome bisulphite sequencing

| PRJNA350687 | ENA

Project description:Assessing the influence of sample tagging and library preparation on DNA metabarcoding

| PRJNA493756 | ENA

scSPLAT

Project description:scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

| PRJEB48307 | ENA

Project description:scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation

| PRJNA774147 | ENA

DNMT3 KO BS seq

Project description:E7.5 embryos from Dnmt3a/3b conditional knock-out mice were isolated, and the epiblast and ectoplacental cone dissected. DNA was isolated from these tissues and BS-seq libraries were generated using the Post-Bisulphite Adaptor Tagging method. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2013-12-09 | E-ERAD-198 | biostudies-arrayexpress

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data

Project description:We performed a parallel analysis of commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se generates pronounced sequencing biases, and subsequent fragmentation and amplification steps lead to several-fold overrepresentation of these artefacts. Standard pre-bisulfite library preparation methods lead to a significantly biased genomic sequence representation and a marked overestimation of methylation levels. We have integrated a bias diagnostic tool in the Bismark package and propose that amplification-free and post-bisulfite procedures should become the gold standard for WGBS library preparation.

2017-02-16 | GSE77961 | GEO

SALP, a new NGS library construction method especially useful for the high-throughput characterization of chromatin openness states

Project description:Background: Next-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. Results: This 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 3ʹ 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 105 to 500 cells. Conclusions: This 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.

2018-01-31 | GSE104162 | GEO

Whole genome bisulphite sequencing using the Illumina X system [Bisulfite-Seq]

Project description:While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads.

2018-07-12 | GSE103503 | GEO

Whole genome bisulphite sequencing using the Illumina X system [Infinium MethylationEPIC]

2018-07-12 | GSE103498 | GEO

Whole genome bisulphite sequencing using the Illumina X system [ATAC-Seq]

2018-07-12 | GSE103301 | GEO