Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

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

PROVIDER: PRJNA350687 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR4453300_1.fastq.gz	Fastqsanger.gz
	SRR4453300_2.fastq.gz	Fastqsanger.gz
	SRR4453291_1.fastq.gz	Fastqsanger.gz
	SRR4453291_2.fastq.gz	Fastqsanger.gz
	SRR4453301_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

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

Homo sapiens

Project description:Optimized adapter:DNA ratios for efficient ChIP-seq library preparation from low input samples

| PRJNA291852 | ENA

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 [Illumina HumanMethylation450 BeadChip]

2018-07-12 | GSE103502 | 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

Project description:New library preparation workflow inspired by DISTAL ligation

| PRJNA1081877 | ENA

Homo sapiens

Project description:ChIP-seq library preparation comparative study

| PRJNA305679 | ENA

Ruler Arrays Reveal Haploid Genomic Structural Variation

Project description:A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence. The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray

2010-09-16 | GSE23524 | GEO

Crystal structure of Homo sapiens kynureninase.

Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

| S-EPMC2531291 | biostudies-literature

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