Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Brassia rapa

ABSTRACT: Comparative studies of ploidy Brassica rapa species.

PROVIDER: PRJNA642307 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12108523_1.fastq.gz	Fastqsanger.gz
	SRR12108523_2.fastq.gz	Fastqsanger.gz
	SRR12108524_1.fastq.gz	Fastqsanger.gz
	SRR12108524_2.fastq.gz	Fastqsanger.gz
	SRR12108525_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Transcriptome analysis for leaf morphology in Brassica rapa

Project description:Among Brassica rapa, rapid cycling Brassica rapa and Brassica rapa inbred line Kenshin showed contrasting leaf morphology. To identify genes associated with leaf morphology, four distinct F2 progeny of RcBr X Kenshin cross and their parents were selected. Leaf samples were collected from 6 materials, isolated total RNA, and subjected to newly developved 135K microarray. Experiments were performed with three or two biologic

2018-05-15 | GSE114479 | GEO

Autopolyploidization-induced chromatin remodeling regulates leaf size variation in Brassica rapa

Project description:Whole-genome duplication (WGD) is an evolutionary event that impacts gene regulation and trait development, but its role in chromatin remodeling and heritable phenotypic changes remains unclear. In this study, employing ATAC-seq, ChIP-seq (H3K4me3, H3K27ac, H3K27me3), and RNA-seq, we examined the epigenomic and transcriptomic dynamics in monoploid, diploid, and autotetraploid B. rapa (Brassica rapa), which share a genome from the same source. Our findings demonstrate that autopolyploidization exerts ploidy-dependent effects on the epigenome and transcriptome, characterized by nonlinear patterns, particularly pronounced during the monoploid-to-diploid transition. Increased ploidy leads to reprogramming chromatin accessibility, characterized by reduced-proximal versus expanded-distal regions. H3K4me3 modifications near transcription start sites alter global gene expression. We identified numerous transcription factor genes, of which BrGRF13 and BrARF11 are crucial to regulate leaf size and polarity during head development. This study is the first to utilize a monoploid system to reveal the mechanisms by which autopolyploidization regulates epigenetic changes through chromatin remodeling, filling a critical knowledge gap and providing novel insights into how polyploidization drives phenotypic variation in plants.

2026-02-18 | GSE308545 | GEO

DNA methylation dynamics in male germline development in Brassica rapa [RNA-seq/Bisulfite-seq]

Project description:Cytosine DNA methylation (mC) can silence transposable elements (TEs) and regulate gene expression. However, the mechanism and function of DNA methylation reprogramming during plant development are still largely unknown. To explore the DNA methylation dynamics during the male sexual-lineage development in the Brassicaceae family, we assessed the mC level in meiocyte, microspore and pollen of a Brassica rapa doubled haploid (DH) line by whole genome bisulfite sequencing (WGBS). Analysis of global mC profiles showed that significant reprogramming of CHH methylation occurred in the Brassica rapa male sex cells, similar to that observed in Arabidopsis. Analysis of differential methylation sites identified specific methylation loci in sex cells that can target and possibly regulate gene expression, suggesting a mechanism consistent with that of Arabidopsis. Quite a few long terminal repeat (LTR) transposable elements were activated in meiocyte and microspore, which correlated with reduced DNA methylation. Expression analysis of key genes that affect DNA methylation showed that active methylation and demethylation occurred during male sexual lineage development. These results suggest a conserved DNA methylation reprogramming mechanism during Brassica rapa male sex lineage development. The transcriptome and DNA methylome data obtained will also be useful for other mechanism studies in Brassica rapa.

2024-09-01 | GSE248075 | GEO

Comparison of root and leaf samples from Brassica rapa

Project description:Root and leaf samples from Brassica rapa line R-O-18 were compared. The results will be compared to the same samples hybridised to the Affymetrix Brassica Exon 1.0 ST array.

2010-09-10 | GSE23409 | GEO

Deep small RNA profiling of anthers of Brassica rapa R-o-18 and rdr2 mutant

Project description:Identifications of small RNAs in anther tissues and compare them with rdr2 mutant of Brassica rapa.

2019-12-01 | GSE141219 | GEO

Brassica rapa chinensis MeJA

Project description:Transcription profiling by array of 10 days old Brassica rapa ssp. chinensis seedlings treated with 2mM methyl jasmonate by spraying and harvesting 48 hours past treatment

2015-01-24 | E-MTAB-2386 | biostudies-arrayexpress

Calcium and Magnesium responses in Brassica rapa

Project description:A mapping population of Brassica rapa (BraIRRI, IMB211xR500) was grown under four external calcium and magnesium concentrations in controlled conditions. RNA was extracted and hybridised to the Affymetrix Brassica Exon 1.0 ST array. The aim of the experiment was to identify cis- and trans- expression quantitative trait loci.

2014-05-21 | GSE44185 | GEO

Genome annotation improvement of Brassica rapa

Project description:The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. Deep RNA-Seq of two Brassica rapa genotypesâR500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)âusing eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. In this experiment, two pools were made, with one pool consisting of 66 samples collected from growth chamber and another pool consisting of 60 samples collected from greenhouse and field. Each pool was sequenced on eight lanes (total 16 lanes) of an Illumina Genome Analyzer (GAIIx) as 100-bp paired end reads.

2014-04-22 | E-MTAB-4276 | biostudies-arrayexpress

A histone methyltransferase, EARLY FLOWERING IN SHORT DAYS (EFS) is required for reproductive organs development via histone H3K36 methylation in the oil-seed type Brassica rapa (B. rapa var. trilocularis) plant.

Project description:We report here NGS RNA-seqencing datasets for two different organ of Brassica rapa plant

2025-06-01 | GSE254671 | GEO

Comparison of root and leaf samples from Brassica rapa

Project description:Root and leaf samples from Brassica rapa line R-O-18 were compared. The results will be compared to the same samples hybridised to the Affymetrix Brassica Exon 1.0 ST array. 6 samples were hybridised. Triplcate samples of 11 day old roots and 2 semi-expanded leaves from 23 day old Brassica rapoa R-O-18 plants.

2010-09-10 | E-GEOD-23409 | 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