Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: DNA methylome and transcriptome sequencing of wild and domesticated soybean

PROVIDER: PRJNA357655 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5117920_1.fastq.gz	Fastqsanger.gz
	SRR5117920_2.fastq.gz	Fastqsanger.gz
	SRR5117930.fastq.gz	Fastqsanger.gz
	SRR5117940_1.fastq.gz	Fastqsanger.gz
	SRR5117940_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 52

Similar Datasets

Characterizing seed weight related genes through transcriptome analyses of wild and cultivated soybeans

Project description:Cultivated soybean has domesticated in China for a long history, and there are several significant phenotypic differences between wild and cultivated soybeans. Seed of cultivar is generally larger than wild soybean, therefore here we comprehensively analyzed transcriptomes of thirteen soybean accessions seeds including seven wild soybeans and six landraces through applying strand-specific RNA sequencing. Differential expressed genes related seed weight were identified, some of them were known to be associated with seed development in Arabidopsis. Noncoding RNAs are known to play important roles in plant development, and we profiled the expression pattern of long noncoding RNA (lncRNA) in cultivated and wild soybean seeds. We have identified 1,251 long intergenic noncoding RNA, 243 intronic RNA and 81 antisense lncRNA, transcriptional levels of a number of lncRNAs were significantly different between cultivated and wild soybeans, suggesting that lncRNA may be involved in soybean seed development.

2017-06-13 | GSE94366 | GEO

Methylation Changes During Soybean Seed Development

Project description:What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation during the transition from seed differentiation to maturation and dormany in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB stage), maturation (early- (EM), mid- (B1) and late- (AA1) maturation stages), and dormancy (DRY stage) phases of soybean seed development using Illumina sequencing. In addition, we characterized the methylome of the mid-maturation stage embryonic axis (B1-AX) to examine methylation differences, if any, between an embryonic region compared to the whole seed. Illumina sequencing of bisulfite-converted genomic DNA from globular stage (GLOB), early-maturation stage (EM), mid-maturation stage (B1), and late-maturation stage (AA1) seeds, dormancy stage (DRY) and mid-maturation embryonic axis (B1-AX).

2011-12-22 | E-GEOD-34637 | biostudies-arrayexpress

Methylation Changes During Soybean Seed Development

Project description:What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation throughout all of seed development - from fertilization through dormancy and post-germination in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB and COT stages), maturation (early- [EM], mid- [B1] and late- [AA1] maturation stages), dormancy (DRY stage), and post-germination (seedling) phases of soybean seed development using Illumina sequencing. In addition, we characterized the methylome of the cotyledons of germinated seedling to examine methylation differences before and after germination.

2011-12-22 | GSE34637 | GEO

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

Project description:Profiling the transcriptome, spliceome, and methylome of developing soybean nodules reveals insights into their associations that may configure transcriptome complexity and proteome diversity

2020-05-22 | GSE135971 | GEO

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

2020-05-22 | GSE135969 | GEO

Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome]

Project description:Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. We confirmed the transcription start sites of genes using high-throughput sequencing and reported the DNA methylation patterns in gene and transposon regions. The correlation between gene expression and DNA methylation was revealed through transcriptome sequencing. We found CHH methylation may function in promotion of gene expression and ten cotyledon-preferred genes were identified CHH hypermethylated in cotyledon. Small RNA library sequencing showed that DNA methylation was enhanced by small RNAs not by strand-specific way, and the variation of DNA methylation between the organs was highly related with expression of small RNAs. methylomes of roots, stems, leaves, and cotyledons of developing seeds

2012-10-30 | E-GEOD-34849 | biostudies-arrayexpress

Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [small RNA]

2012-10-30 | GSE34853 | GEO

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

Project description:We report total mRNA library using Illumina Nova Seq high-throughput sequencing platform platform for analysis of transcriptome between the two relatives of the soybean ie weedy and cultivar growth types in F7 generation derived from the crossing of wild and cultivated soybean.

2021-11-12 | GSE188519 | GEO

Project description:Transcriptome sequencing from wild and domesticated eggplant

| PRJNA526115 | ENA

Multiple-omics studies of pear fruit flesh

Project description:A comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening.

2024-02-02 | PXD049025 |

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