Mapping and dynamics of regulatory DNA in A. thaliana accessions
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: John Stamatoyannopoulos
PROVIDER: E-GEOD-53323 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We performed DNase-seq on 7-day-old seedlings from four A. thaliana accessions: Bur-0, Tsu-0, Bay-0, Est-1 using INTACT constructs (Deal and Henikoff, Developmental Cell, 2010) driven by the UBQ10 promoter.
2013-12-15 | GSE53323 | GEO
Project description:We performed DNase-seq on root tissue, root epidermal cell types, seed coat epidermal cells at two developmental stages, and open and closed flowers. Root: We performed chromatin profiling (DNase-seq) on whole root (all cell types), or root epidermal cell types (hair cell, non-hair cell). Seed coat: We performed chromatin profiling on seed coat epidermal cells from siliques at two developmental stages (4 days past anthesis, 7 days past anthesis). We preformed chromatin profiling (DNase-seq) on flowers at two developmental time points (open and closed flowers). All plants were grown on plates (roots only) or in soild in LD conditions (16hr light 22°C, 8hr dark 20°C). The following processed data files are pooled short read data from 2 biological replicates (GSM1289379 [DS21306] and GSM1824051 [DS20134]): Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.signal.bw Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.8M.peaks.bed Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.signal.bw Col-0.Seed_Coat.Seed_Coat_7DPA.DNase.pooled.6.65M.peaks.bed The following processed data files are pooled short read data from 2 biological replicates (GSM1824052 [DS20131] and GSM1824053 [DS20132]): Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.signal.bw Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.8M.peaks.bed Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.signal.bw Col-0.Seed_Coat.Seed_Coat_4DPA.DNase.pooled.6.65M.peaks.bed The following processed data files are pooled pooled short read data from 2 biological replicates (GSM1824054 [DS19056] and GSM1824055 [DS21512]): Col-0.Root.Hair.DNase.pooled.6.8M.signal.bw Col-0.Root.Hair.DNase.pooled.6.8M.peaks.bed
2013-12-15 | E-GEOD-53324 | biostudies-arrayexpress
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). Examination of RNA expression across tissues (seedling, root, floral bud) for 17 Arabidopsis thaliana accessions (Bur-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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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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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
Project description:We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. Analysis of >700,000 TF footprints disclosed an extensive cis-regulatory lexicon, and enabled construction of large-scale TF cross-regulatory networks. Although the cis- and trans-regulatory repertoire is markedly distinct from mammals, the architecture of A. thaliana TF networks is strikingly similar to those of human. Analysis of the DHS landscape and TF network dynamics during heat shock and photomorphogenesis revealed thousands of conditionally-sensitive elements and enabled mapping of key regulatory circuits. Our results provide an extensive resource for understanding and enabling diverse aspects of A. thaliana biology. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old dark-grown seedlings exposed to 0hr light, 30min light, 3hr light or 24hr LD conditions. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old LD-grown seedlings treated with a brief sever heat shock or kept under control conditions. Replicates are included when available; controls and read-normalized samples (samples that were subsampled to the same read-depth) are also included here.
2013-12-15 | E-GEOD-53322 | biostudies-arrayexpress
Project description:Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50 % of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0. The microarray analysis was used to identify candidate genes for Cd-tolerance and -accumulation differences between the accessions Bur-0 and Col-0 as well as to analyse the expressional response of A.thaliana to Cd-stress.
2017-07-24 | GSE94314 | GEO
Project description:Alternative splicing (AS) plays key roles in plant development and responses to environmental changes. However, the mechanisms underlying AS divergence (differential expression of transcript isoforms resulting from alternative splicing) in plant accessions and its contributions to responses to environmental stimuli remain unclear. In this study, we investigated genome-wide variation of AS in Arabidopsis thaliana accessions Col-0, Bur-0, C24, Kro-0, and Ler-1, as well as their F1 hybrids, and characterized the regulatory mechanisms for AS divergence by RNA sequencing (RNA-seq). We found that most of the divergent AS events in Arabidopsis accessions were cis-regulated by sequence variation, including those in core splice site and splicing motifs. Many genes that differed in AS between Col-0 and Bur-0 were involved in stimulus responses. Further genome-wide association analyses of 22 environmental variables showed that SNPs influencing known splice site strength were also associated with environmental stress responses. These results demonstrate that cis-variation in genomic sequences among Arabidopsis accessions was the dominant contributor to AS divergence, and it may contribute to differences in environmental responses among Arabidopsis accessions.
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Project description:We report the identification of parent-of-origin specific gene expression in Arabidopsis seeds. F1 hybrid seeds were generated by reciprocally crossing Arabidopsis accessions Col-0 and Bur-0. Seeds were harvested at 4 DAP and total RNA was isolated and analyzed by deep sequencing. Overall identification of parent-of-origin-allelic expression by analysis of SNP distribution
2011-04-30 | E-GEOD-27292 | biostudies-arrayexpress