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Brassica rapa

ABSTRACT: Elucidation of stress memory inheritance through epigenome alterations in Brassica rapa plants [RNA-seq]

OTHER RELATED OMICS DATASETS IN: GSE58897

PROVIDER: PRJNA253868 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1485200.fastq.gz	Fastqsanger.gz
	SRR1485210.fastq.gz	Fastqsanger.gz
	SRR1485220.fastq.gz	Fastqsanger.gz
	SRR1485201.fastq.gz	Fastqsanger.gz
	SRR1485211.fastq.gz	Fastqsanger.gz

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Brassica rapa

Project description:Elucidation of stress memory inheritance through epigenome alterations in Brassica rapa plants [small RNA-seq]

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Comparison of root and leaf samples from Brassica rapa

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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.

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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.

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