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Arabidopsis thaliana

ABSTRACT: Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

PROVIDER: PRJNA239720 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR1179960_1.fastq.gz	Fastqsanger.gz
	SRR1179960_2.fastq.gz	Fastqsanger.gz
	SRR1179970_1.fastq.gz	Fastqsanger.gz
	SRR1179970_2.fastq.gz	Fastqsanger.gz
	SRR1179980_1.fastq.gz	Fastqsanger.gz

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Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

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Project description:Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

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Transcriptomes for hybrids (F1s) between 18 Arabidopsis thaliana parents of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource

Project description:We produced RNA-Seq reads from messenger RNA isolated from aerial seedling tissue for 9 hybrids (F1s) generated by crossing in a pairwise manner 18 of the founding accessions (inbred strains) of the Multiparent Advanced Generation Inter-Cross (MAGIC) genetic mapping resource for 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 provides a resource to assess allele-specific gene expression between A. thaliana accessions. With 18 of the MAGIC parental inbred accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) crosses were performed to generate 9 sets of F1 progeny from which RNA was extracted with biological replication (three replicates) and for which mRNA-seq was performed to generate strand-specific reads. Library construction and sequencing was performed such that each set of biological replicates were sequenced as a pool (with 9-plex barcoding; each 9-plex was run on two HiSeq lanes).

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Project description:To understand expression phenotypes in Arabidopsis thaliana at high temperature, a set of the Multiparent Advanced Generation Inter-Cross (MAGIC) recombinant inbred lines were grown under long day conditions (16 hours light: 8 hours dark) at 20˚C and then shifted to 30˚C for 48 hours. RNA was collected at the 4th true leaf stage, and RNA-seq data was generated using the Illumina method. The MAGIC lines included are largely a subset of lines for which comparable RNA-seq data was collected at a constant 20˚C (allowing the same genotypes to be compared at 20˚C and after the high temperature shift at approximately the same developmental stage and under otherwise the same growth conditions). The read data for the analogous low temperature study can be found under GEO submission GSE94107.

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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). Examination of RNA expression in root for the 19 Arabidopsis thaliana accessions used as parents for the MAGIC lines (parental accessions are Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, Zu-0).

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