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

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Richard Clark

PROVIDER: E-GEOD-30720 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Gan Xiangchao X Stegle Oliver O Behr Jonas J Steffen Joshua G JG Drewe Philipp P Hildebrand Katie L KL Lyngsoe Rune R Schultheiss Sebastian J SJ Osborne Edward J EJ Sreedharan Vipin T VT Kahles André A Bohnert Regina R Jean Géraldine G Derwent Paul P Kersey Paul P Belfield Eric J EJ Harberd Nicholas P NP Kemen Eric E Toomajian Christopher C Kover Paula X PX Clark Richard M RM Rätsch Gunnar G Mott Richard R

Nature 20110828 7365

Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accessio ...[more]

PMID: 21874022

Similar Datasets

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.

2011-08-29 | GSE30720 | GEO

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).

2013-12-11 | GSE53197 | GEO

Multiple tissue RNA sequencing of 17 Arabidopsis thaliana MAGIC founder accessions

2013-12-11 | E-GEOD-53197 | biostudies-arrayexpress

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. Examination of RNA expression across tissues (seedling, root, floral bud) for 2 accessions (Col-0, Can-0).

2011-08-29 | E-GEOD-30795 | biostudies-arrayexpress

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).

2013-12-11 | GSE53198 | GEO

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

2013-12-11 | E-GEOD-53198 | biostudies-arrayexpress

Multiple tissue RNA sequencing of two Arabidopsis thaliana MAGIC founder accessions

2011-08-29 | GSE30795 | GEO

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

2014-03-01 | GSE55482 | GEO

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).

2014-03-01 | E-GEOD-55482 | biostudies-arrayexpress