Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Comparison of read length between two library preparation methods for whole-genome bisulfite sequencing

PROVIDER: PRJNA486097 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7695474_1.fastq.gz	Fastqsanger.gz
	SRR7695474_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Whole genome DNA methylation profiling of D2 medium spiny neurons in mouse nucleus accumbens using two independent library preparation methods

Project description:We isolated genomic DNA from adult male mouse nucleus accumbens (NAc) D2 medium spiny neurons (D2-MSN) by fluorescence-activated cell sorting. We performed the whole genome methylation profiling using two independent library preparation methods, namely the sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq) of Swift biosciences and the enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq) from New England Biolabs, on two identical samples. We mapped about 400 million paired-end reads to the mouse genome (build mm10) and assessed measures of each methylome by two methods. This study provided a side-by-side comparison of two independent whole genome profiling methods for low-input neuronal samples.

2022-03-04 | GSE195752 | GEO

Project description:Comparison of sensitivities and mapping efficiencies of two library preparation methods.

| PRJNA523642 | ENA

Escherichia coli

Project description:Library preparation methods development

| PRJNA565026 | ENA

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 methylome data obtained with rPBAT and tPBAT.

Project description:To compare the difference of library preparation protocols for whole-genome bisulfite sequencing, two libraries were prepared from genomic DNA extracted from IMR90 cell with rPBAT and tPBAT. Two and tree lanes of HiSeq X Ten were assigned for tPBAT and rPBAT libraries, respectively

2018-08-28 | GSE119069 | GEO

Comparison of library preparation methods

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

| PRJEB7411 | ENA

Project description:Comparison of RO-seq Isolation Protocols and Library Preparation Methods

| PRJNA722106 | ENA

Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling

Project description:Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling, however the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read non-destructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter we provide a detailed protocol for preparation, sequencing, read assembly and analysis of genome-wide 5mC using Nanopore sequencing technologies.

2021-12-03 | GSE179673 | 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

Loss of Asxl2 leads to myeloid malignancies in mice. [RNA-Seq]

Project description:Total RNA was isolated from mouse Asxl2-/- and WT LK cells following standard protocol with TRIZol reagent (Life Technologies) followed by RNA library preparation with the Illumina TruSeq strand-specific mRNA sample preparation system. All RNA-seq libraries were sequenced with a read length of single-end 75bp using the Illumina NextSeq 500, and final of over 45 million reads per sample.

2018-03-08 | GSE97021 | GEO

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