Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA300452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2850580.fastq.gz | Fastqsanger.gz | |||
| SRR2850590.fastq.gz | Fastqsanger.gz | |||
| SRR2850600.fastq.gz | Fastqsanger.gz | |||
| SRR2850571.fastq.gz | Fastqsanger.gz | |||
| SRR2850581.fastq.gz | Fastqsanger.gz |
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Project description:Background: The carpel margin meristem is a vital multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results: Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter construct, paired with fluorescence-activated cell sorting, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. Our analysis reveals a set of genes that are differentially-expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members of this gene set, including a set of differentially-expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development and candidates for future functional studies. Several members of the REM family of transcriptional regulators were enriched in the SHP2-expressing cell population including a previously unrecognized REM family member (At5g60142). Analysis of the abundance of specific transcriptional isoforms identified genes that may exhibit âisoform switchingâ behavior during gynoecial development. Conclusions: This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, an important reproductive structure that gives rise to the ovules in Arabidopsis thaliana. Four samples (YFP-positive, YFP-negative, all-sorted, and non-sorted). Four biological replicates of each sample (except YFP-positive, collected in triplicated). Strand-specific libraries were sequenced (single-end) in two lanes of a HiSeq 2500 Illumina flow cell (each lane was later analyzed as a technical replicate).
2016-02-29 | E-GEOD-74458 | biostudies-arrayexpress
Project description:Background: The carpel margin meristem is a vital multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results: Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter construct, paired with fluorescence-activated cell sorting, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. Our analysis reveals a set of genes that are differentially-expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members of this gene set, including a set of differentially-expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development and candidates for future functional studies. Several members of the REM family of transcriptional regulators were enriched in the SHP2-expressing cell population including a previously unrecognized REM family member (At5g60142). Analysis of the abundance of specific transcriptional isoforms identified genes that may exhibit “isoform switching” behavior during gynoecial development. Conclusions: This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, an important reproductive structure that gives rise to the ovules in Arabidopsis thaliana.
2016-02-29 | GSE74458 | GEO
Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Experiment Overall Design: Three replicates were used CLV3p, CLV3n and FILp, while for WUSp only two replicates were used. CLV3n cells lacks CLV3p cell type.
2009-04-11 | E-GEOD-13596 | biostudies-arrayexpress
Project description:A gene expression map of Arabidopsis thaliana shoot apical meristem stem cell niche was generated by isolating the specific cell type using the cell sorting methods. We used ap1-1;cal1-1 mutant background to enrich the sufficient number of cells for microarray analysis. Spatial and temporal regulation of gene expression is critical for stem-cell homeostasis. The shoot apical meristems of Arabidopsis thaliana harbor a small set of stem-cells which are surrounded by several million differentiating cells, imposing a severe limitation on the genomic analyses of stem-cell homeostasis. We have employed cell type-specific gene expression profiling that allowed us to generate a high-resolution gene expression map and it has revealed gene expression networks specific to the cell types of the stem-cell niche. We demonstrate that the expression map can be used to predict in vivo gene expression domains to identify novel gene expression patterns. Furthermore, it has revealed molecular pathways that are conserved among plant and animal stem-cell populations. The expression map should guide future reverse genetics experiments, high-resolution analyses of cell-cell communication networks and epigenetic modifications. Keywords: cell type comparison
2009-04-06 | GSE13596 | GEO
Project description:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Keywords: Development time course
2007-05-17 | GSE6893 | GEO
Project description:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Experiment Overall Design: Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.
2008-11-08 | E-GEOD-6893 | biostudies-arrayexpress
Project description:Time course of the Arabidopsis thaliana root meristem
| PRJNA383074 | ENA
Project description:At the transition from vegetative to reproductive growth in rice, a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem (SAM) to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor. APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites by ChIP-seq analysis. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation at the reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.
2024-04-09 | GSE263431 | GEO
Project description:The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity.
2011-12-07 | GSE34209 | GEO
Project description:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been described. In this study we analyzed gene expression during Arabidopsis thaliana meristem development from day 7 to 16 after germination in one-day increments. The dynamics of the expression of the main flowering regulators were consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. GO enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle, suggesting that during transition to the flowering stage a change in dynamics of cell division takes place. In particular, we hypothesize that a subset of the meristematic cells experiences a forced exit from G0 at day 10. Finally, we observed an acceleration of the cell cycle at day 11, which may be linked to meristem reorganization preceding activation of LFY.
2015-07-21 | E-MTAB-4202 | biostudies-arrayexpress