Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Glycine max

ABSTRACT: Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs (MethylC-seq)

PROVIDER: PRJNA354570 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5044700_1.fastq.gz	Fastqsanger.gz
	SRR5044700_2.fastq.gz	Fastqsanger.gz
	SRR5044693_1.fastq.gz	Fastqsanger.gz
	SRR5044693_2.fastq.gz	Fastqsanger.gz
	SRR5044694_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs (MethylC-seq)

Project description:Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. Since root hairs are single cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single cell root hairs as compared to multi-cellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated as compared to stripped roots. However, in response to heat stress, both root hairs and stripped roots showed more hypomethylation in each context, especially in the mCHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes of dynamic DNA methylation directly or indirectly is associated with expression of genes and transposons either within the context of specific tissues/cells or stress (heat).

2017-08-01 | GSE90142 | GEO

Epigenomics of Glycine max

Project description:Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Glycine max lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.

2018-05-07 | GSE114074 | GEO

Transcriptomic profiling of brassinosteroids response genes in soybean (Glycine max L.)

Project description:Brassinosteroids (BRs) are a series of sterol hormones in plants, which play important physiological roles in many aspects of plant growth and development processes. Exogenous application of BR and its inhibitors PPZ to investigated the roles of BR in soybean root growth and development. Transcriptome sequencing analysis was performed to identified lots number of differential expression genes(DEGs) by eBL (2,4-epicastasterone, 24-epiCS) and PPZ (propiconazole) treatment of soybean root tips(1 cm).

2021-05-28 | GSE175586 | GEO

Phosphoproteomic sequencing of Glycine max under alkali stress

Project description:Alkali stress is one of the most severe abiotic stresses affecting agricultural production worldwide. To understand the phosphorylation events in soybean in response to alkali stress, we performed the TMT labeling-based quantitative phosphoproteomic analyses on soybean leaf and root tissues under 50 mM NaHCO3 treatment.

2024-01-26 | PXD041842 | Pride

Glycine max Transcriptome or Gene expression

Project description:Intercropping is a sustainable agricultural practice widely used around the world for enhancing resource use efficiency. However, short crops often grow in shade condition underneath the canopy of tall crops. Soybean is one of the most important oil crops and usually is planted in intercropping patterns. However, little is known about the acclimation responses of soybean leaves to shade in intercropping condition at the transcriptome level.

2013-07-11 | E-MTAB-4279 | biostudies-arrayexpress

Expression data of Soybean (Glycine max) roots from different iron treatments.

Project description:Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate. After 10 days, half the plants were harvested (total root tissue). At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions. Root tissue was harvested for the remaining plants at 14 days after planting. Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions.

2010-09-06 | GSE22227 | GEO

Glycine max

Project description:Flux of transcript patterns during soybean seed development

| PRJNA121455 | ENA

Genome level identification of transcription start sites by nanoCAGE sequence in soybean (Glycine max).

Project description:Identification of the transcription start sites (TSS) of genes is critical for understanding promoter regions and transcription initiation. One well characterized and widely used method to determine TSSs is CAGE (Cap Analysis of Gene Expression). CAGE has been commonly used in animal studies, yet in plants species, the precise TSS and core promoter landscape is not sufficient yet, no experiment has been taken on soybean to identify TSS neither. Soybean is one economically valuable species used for both food supply and oil. In this study, we present the main results of nanoCAGE-seq to reveal the genome-wide TSS conducted on shoot and root in soybean Williams 82.

2025-08-28 | GSE302313 | GEO

Glycine max

Project description:Methylation Changes During Soybean Seed Development

| PRJNA151265 | ENA

Glycine max

Project description:Single-base resolution DNA methylomes of soybean recombinant inbred lines reveals heritability patterns of natural methylation variants

| PRJNA178155 | ENA

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