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Arabidopsis MAGIC

ABSTRACT: Low-Coverage sequence of Arabidopsis MAGIC Genomes

OTHER RELATED OMICS DATASETS IN: E-GEOD-30720GSE30814

PROVIDER: PRJEB19252 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR1869600.fastq.gz	Fastqsanger.gz
	ERR1869600_1.fastq.gz	Fastqsanger.gz
	ERR1869600_2.fastq.gz	Fastqsanger.gz
	ERR1869610.fastq.gz	Fastqsanger.gz
	ERR1869610_1.fastq.gz	Fastqsanger.gz

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ARABIDOPSIS MAGIC RESEQUENCING

Project description:Low coverage sequence data from 476 Arabidopsis MAGIC lines and high coverage data from 9 MAGIC lines

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An RNA-seq dataset for studies of gene expression variation in the MAGIC line resource of Arabidopsis thaliana

Project description:To understand the population genetics of structural variants (SVs), and their effects on phenotypes, we developed an approach to mapping SVs, particularly transpositions, segregating in a sequenced population, and which avoids calling SVs directly. The evidence for a potential SV at a locus is indicated by variation in the counts of short-reads that map anomalously to the locus. These SV traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between an SV trait at one locus and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3x) population sequence data from 488 recombinant inbred Arabidopsis genomes, we identified 6,502 segregating SVs. Remarkably, 25% of these were transpositions. Whilst many SVs cannot be delineated precisely, PCR validated 83% of 44 predicted transposition breakpoints. We show that specific SVs may be causative for quantitative trait loci for germination, fungal disease resistance and other phenotypes. Further we show that the phenotypic heritability attributable to sequence anomalies differs from, and in the case of time to germination and bolting, exceeds that due to standard genetic variation. Gene expression within SVs is also more likely to be silenced or dysregulated, as inferred from RNA-seq data collected from a subset of just over 200 of the MAGIC lines. This approach is generally applicable to large populations sequenced at low-coverage, and complements the prevalent strategy of SV discovery in fewer individuals sequenced at high coverage.

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Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

Project description:We produced RNA-Seq reads from messenger RNA isolated from seedling, root, and floral bud tissue for 17 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provide a resource to assess tissue-specific expression across different accessions of A. thaliana. Note that comparable read data for accessions Col-0 and Can-0, which are also founders of the MAGIC lines, has previously been released under GEO series GSE30795 (Gan et al. 2011. Nature, 477:419-23).

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Root transcriptomes for the 19 parents of the Arabidopsis thaliana MAGIC lines

Project description:We produced RNA-Seq reads from messenger RNA isolated from root tissue for the 19 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature 477:419-23 for a description of the MAGIC genetic mapping resource). The read data was generated with biological replication (two replicates). The resulting RNA-Seq data provide a resource to assess root gene expression across different accessions of A. thaliana. Comparable RNA-Seq read data for the MAGIC founder accessions for aerial seedling tissue has previously been released under GEO series GSE30720 (Gan et al. 2011. Nature, 477:419-23).

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Multiple tissue RNA sequencing of two Arabidopsis thaliana MAGIC founder accessions

Project description:We sequenced messenger RNA isolated from seeding, root, and floral bud tissue for 2 MAGIC founder accessions of Arabidopsis thaliana. The resulting data was used for validation of gene models, and provides a resource to assess tissue-specific expression.

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Project description:We have sequenced messenger RNA isolated from seedling tissue for 19 accessions of Arabidopsis thaliana (with biological replication). The 19 accessions for which RNA-Seq reads were collected have served as the founders for the MAGIC lines, a high-resolution recombinant inbred line mapping resource. RNA sequencing data was used to examine differential gene expression among the accessions.

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Root transcriptomes for the 19 parents of the Arabidopsis thaliana MAGIC lines

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Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

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