Ontology highlight
ABSTRACT:
PROVIDER: PRJNA587058 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10382515_1.fastq.gz | Fastqsanger.gz | |||
| SRR10382515_2.fastq.gz | Fastqsanger.gz | |||
| SRR10382516_1.fastq.gz | Fastqsanger.gz | |||
| SRR10382516_2.fastq.gz | Fastqsanger.gz | |||
| SRR10382517_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:This experiment was designed to identify genes expressed preferentially in the two integuments of the Arabidopsis ovule. Pistils from wild type and two ovule mutants were compared against each aintegumenta-4 (ant-4) which lacks both integuments and inner no outer (ino-1) which lacks the outer integument. Genes that are highly expressed only in the integuments were expected to be reduced in expression in the mutants, as compared with wild type. Pistils containing ovules through all stages of ovule development prior to pollination were pooled for one experiment (FULL arrays), and for two separate experiments, a set of early differentiation stages (EARLY arrays) and a set of later differentiation stages (LATE ARRAYS) were pooled. Wild type and mutant lines are in the ecotype Landsberg erecta.
2009-06-01 | E-MEXP-1920 | biostudies-arrayexpress
Project description:The transcriptome of outer integument of canola seed coat was compared to seven day old canola hypocotyls using the Brassica 90kCombimatrix microarray
2010-09-01 | E-MEXP-2103 | biostudies-arrayexpress
Project description:Ovule developmental arrest is one of the early phenotypes of seed abortion. However, the molecular mechanism underlying ovule developmental arrest of citrus is still unclear. In this study, laser capture microdissection (LCM) was used to accurately divide the ovules of seedless Ponkan ‘Huagan NO.4’ (Citrus reticulata) (MT) and seeded Ponkan ‘Egan NO.1’ (Citrus reticulata) (WT) into nucellus and integument tissues. The captured tissues were used for subsequent RNA-seq. Moreover, single-molecule real-time (SMRT) sequencing was used to generate full-length transcripts of WT, which were used as reference transcripts for RNA-seq. These data can be utilized to analyse the causes of citrus seedlessness formation and the molecular regulatory network in the process of ovule abortion.
2024-09-01 | GSE183639 | GEO
Project description:Ovule development is a key process for plant reproduction that ensures correct seed production. Understanding the molecular mechanisms that control ovule formation will also provide new approaches to increase crop yield for breeding. Several molecular factors and plant hormones, including gibberellins, are involved in ovule initiation and development. Gibberellins control ovule development by the destabilization of DELLA proteins, whereas DELLA activity has been proved to act as a positive factor for ovule primordia emergence. But the molecular mechanism by which DELLA act remained unknown. Here we have proved that DELLA proteins control ovule initiation by the formation of a protein complex with the CUC2 transcription factor. The DELLA protein GAI requires CUC2 to promote ovule primordia formation, thus GAI would function by its direct protein-protein interaction with CUC2 in cells of the placenta that determine the boundary regions between ovules during pistil development. Analysis of GAI-CUC2 interaction and colocalization in placenta support this hypothesis. Moreover, molecular analysis of the loci at which GAI protein may act as transcriptional co-regulators in a CUC2-dependent manner identified a subset of target genes that would be regulated by the GAI-CUC2 complex and contribute to regulate ovule primordia emergence.
2021-12-23 | GSE178414 | GEO
Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification
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Project description:To assess further the role of CYN in relation to integument morphogenesis, gametophytic cell fate specification, embryogenesis and endosperm development, we compared the expression profiles between the cyn mutant and wild-type at two different stages(before flowering and 5 days after pollination stage) of ovule development by microarray analysis. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as auxin efflux & polarity & cell differentiation, flower and embryonic development, signal transduction.These results supported that MADS protein CYN could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes (including MADS or non-MADS transcription factors) involved in developmental and hormonal pathways. Three independent biological replicates of cyn mutant and wild-type panicle mRNA at two different stages of ovule development were used for microarray experiments. To perform microarray analysis, the samples were pooled by 20 panicles from 10 individual plants at before flowering and 5 days after pollination stage.
2014-11-03 | E-GEOD-33441 | biostudies-arrayexpress
Project description:To assess further the role of CYN in relation to integument morphogenesis, gametophytic cell fate specification, embryogenesis and endosperm development, we compared the expression profiles between the cyn mutant and wild-type at two different stages(before flowering and 5 days after pollination stage) of ovule development by microarray analysis. Specifically, we confirmed significant changes of up- or down-regulation in some genes required for several biological processes, such as auxin efflux & polarity & cell differentiation, flower and embryonic development, signal transduction.These results supported that MADS protein CYN could function both as a transcriptional activator and repressor, directly and/or indirectly interacted with dozens of potential target genes (including MADS or non-MADS transcription factors) involved in developmental and hormonal pathways.
2014-11-03 | GSE33441 | GEO
Project description:Ovule formation is essential for realizing crop yield as it determines seed number. The underlying molecular mechanism, however, remains elusive. Here, we show that cell wall invertase (CWIN) functions as a positive regulator of ovule initiation in Arabidopsis. In situ hybridization revealed that CWIN2 and CWIN4 were expressed at the placenta region where ovule primordia initiated. Specific silencing of CWIN2 and 4 by using targeted artificial microRNA driven by an ovule-specific SEEDSTICK promoter (pSTK) resulted in a significant reduction of CWIN transcript and activity, which blocked ovule initiation and aggravated ovule abortion. Surprisingly, there was no induction of carbon starvation genes in the transgenic lines and supplement of extra carbon to newly forming floral buds failed to recover the ovule phenotype. The findings indicate that suppression of CWIN did not lead to carbon starvation. Interestingly, a group of hexose transporters was downregulated in the transgenic plants and two representative transporter genes, STP9 and SWEET8 were spatially co-expressed with CWIN2 and CWIN4, suggesting a coupling between CWIN and hexose transporters for ovule initiation. RNA-Seq analysis identified differentially expressed genes encoding putative extracellular receptor-like-kinases (RLKs), MADS-box transcription factors including STK and early auxin response genes, SAURs, in response to CWIN-silencing. Collectively, our data demonstrate the essential role that CWIN plays in ovule initiation likely through sugar signalling instead of carbon nutrient contribution. We propose that CWIN-mediated sugar signalling may be perceived by, and transmitted through, hexose transporters or RLKs to regulate ovule formation by modulating downstream auxin signalling and MADS-box transcription factors.
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Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
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