Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS]

ABSTRACT: Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS]

PROVIDER: PRJNA528657 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9888310_1.fastq.gz	Fastqsanger.gz
	SRR9888310_2.fastq.gz	Fastqsanger.gz
	SRR9888320_1.fastq.gz	Fastqsanger.gz
	SRR9888320_2.fastq.gz	Fastqsanger.gz
	SRR9888330_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 82

Similar Datasets

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS]

Project description:We systematically evaluated alternate strategies for WGBS studies, taking into account opportunites around library preparation methods, sequencing platforms and analysis pipeline optimization. We also assessed the performance and precision of the WGBS method relative to the methylation arrays, in an effort to provide data-driven recommendations for future WGBS studies, in particularly with respect to minimum coverage.

2019-07-29 | GSE128731 | GEO

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [Beadchip]

2019-07-29 | GSE128733 | GEO

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

Project description:Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

| PRJNA528654 | ENA

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

Project description: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.

2016-10-27 | GSE89213 | GEO

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [Beadchip]

Project description:Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [Beadchip]

| PRJNA528685 | ENA

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-07-29 | GSE128734 | GEO

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing.

Project description:Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efficient WGBS for application in future large-scale epidemiological studies. We systematically compared the performance of three WGBS library preparation methods with low DNA input requirement (Swift Biosciences Accel-NGS, Illumina TruSeq and QIAGEN QIAseq) on two state-of-the-art sequencing platforms (Illumina NovaSeq and HiSeq X), and also assessed concordance between data generated by WGBS and methylation arrays. Swift achieved the highest proportion of CpG sites assayed and effective coverage at 26x (P < 0.001). TruSeq suffered from the highest proportion of PCR duplicates, while QIAseq failed to deliver across all quality metrics. There was little difference in performance between NovaSeq and HiSeq X, with the exception of higher read duplication rate on the NovaSeq (P < 0.05), likely attributable to the higher cluster densities on its flow cells. Systematic biases exist between WGBS and methylation arrays, with lower precision observed for WGBS across the range of depths investigated. To achieve a level of precision broadly comparable to the methylation array, a minimum coverage of 100x is recommended.

| S-EPMC6637168 | biostudies-literature

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

Comparison of library preparation methods

Project description:Comparison of library preparation methods using Cryptococcus neoformans var. grubii

| PRJEB7411 | ENA

Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods

Project description:Many library preparation methods are available for gene expression quantification. Here, we sequenced and analysed Universal Human Reference RNA (UHRR) prepared using Smart-Seq2, TruSeq (public data) and a protocol using unique molecular identifiers (UMIs) that all include the ERCC spike-in mRNAs to investigate the effects of amplification bias on expression quantification. UHRR 10 and 12 replicates for Smart-seq2 and UMI-seq library preparation methods, respectively.

2016-05-13 | E-GEOD-75823 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data