Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Arabidopsis thaliana WGBS data for methhap performance test

PROVIDER: PRJNA543389 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9077100_1.fastq.gz	Fastqsanger.gz
	SRR9077100_2.fastq.gz	Fastqsanger.gz
	SRR9077101_1.fastq.gz	Fastqsanger.gz
	SRR9077101_2.fastq.gz	Fastqsanger.gz
	SRR9077102_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Methylated DNA is over-represented in whole-genome bisulfite sequencing data

Project description:The development of whole-genome bisulfite sequencing (WGBS) has led to a number of exciting discoveries about how genomes utilize DNA methylation and has led to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently excelled to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of methylated DNA from WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. MethylC-Seq of Arabidopsis thaliana

2014-09-11 | E-GEOD-58217 | biostudies-arrayexpress

MPLEx_Arabidopsis_thaliana

Project description:Datasets of Arabidopsis thaliana samples used to test the MPLEx method

2015-12-03 | MSV000079405 | MassIVE

WGBS of Arabidopsis thaliana rll6 mutant

Project description:WGBS of Arabidopsis thaliana rll6 mutant

| PRJNA859377 | ENA

Arabidopsis thaliana 25 accessions

Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.

2018-11-14 | ST001096 | MetabolomicsWorkbench

WGBS of Arabidopsis thaliana COM-edm2 mutant

Project description:WGBS of Arabidopsis thaliana COM-edm2 mutant

| PRJNA956973 | ENA

Small-RNA sequencing of WUS-induced RNA degradation in Arabidopsis thaliana

Project description:WUS is the key regulator in stem cell induction and maintenance. We performed the small RNA high throughput sequencing to test whether WUS is involved in stabilizing RNA structure in Arabidopsis thaliana.

2022-03-25 | GSE128779 | GEO

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

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 | GSE128733 | GEO

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

2019-07-29 | GSE128731 | GEO

Global methylation in Arabidopsis plants after multigenerational exposure to high temperatures

Project description:We conducted whole-genome bisulfite sequencing (WGBS) of Arabidopsis thaliana mutation accumulation (MA) lines under different temperature treatments over sucessive generations, and then we identified the global methylation in each MA line. Our result showed taht DNA methylation was observed more frequently at DNA mutation sites, indicating its contribution to the mutation process at elevated temperatures.

2021-05-01 | GSE173660 | GEO

High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

Project description:In this study, we combine MspJI digestion and electrophoretic band selection with next generation high-throughput sequencing technology to detect 5-methylcytosines in Arabidopsis genome. By developing a bioinformatics workflow to attribute the CNNR sites recognized by MspJI to the reference genome, we fulfilled the systematic assessment of this method. According to the assessment, here we provide the method for generating a detailed map of plant methylome that could be feasible, reliable and economical in methylation investigation. Extracting the MspJI digested fragments, constructing sequencing library according to the Illumina protocol and sequencing with Illumina HiSeq2000. Repeatability and reproducibility studies were performed between two samples from the same individual. Specificity and sensitivity of the method was examined by comparing our data with WGBS data downloaded from GEO (GSE15922: GSM399600). **The WGBS seq data ('aerial_tissues_BS_seq_CNNR.gff') was generated from the GSM399600 Sample supplementary files ('aerial_tissues_BS_seq_alignment_batch-*.gff.gz') and was utilized to do comparative study with our MspJI-seq data including sensitivity and specificity analysis.

2013-05-01 | E-GEOD-46428 | 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