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Seedling transcriptome sequencing of the Arabidopsis thaliana MAGIC founder accessions

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE30720 | GEO | 2011/08/29

SECONDARY ACCESSION(S): PRJNA154687

REPOSITORIES: GEO

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Seedling transcriptome sequencing of the Arabidopsis thaliana MAGIC founder accessions

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. Examination of RNA expression in seedling tissue carried out using biological replicates.

2011-08-29 | E-GEOD-30720 | biostudies-arrayexpress

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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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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