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E-MTAB-9569

ABSTRACT: Transcriptome profile of Arabidopsis thaliana wild-type versus mea mutant ovary and seed at different developmental time points

TISSUE(S): Seed, Plant Ovary

PROVIDER: E-MTAB-9569 | ExpressionAtlas | 2021-01-15

REPOSITORIES: ExpressionAtlas

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Dataset's files

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			Action	DRS
	E-MTAB-9569-analysis-methods.tsv	Tabular
	E-MTAB-9569-analytics.tsv	Tabular
	E-MTAB-9569-apply_fixes_zooma_mappings.done	Other
	E-MTAB-9569-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-9569-configuration.xml	Xml

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Transcriptome profile of Arabidopsis thaliana wild-type versus mea mutant ovary and seed at different developmental time points

Project description:Transcriptome profile of Arabidopsis thaliana wild-type versus mea mutant ovary and seed at different developmental time points

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Transcriptome profile of Arabidopsis thaliana wild-type versus mea mutant ovary and seed at different developmental time points

Project description:merMEDEA (MEA) is a component of the Polycomb Repressive complex 2 (PRC2) of Arabidopsis thaliana, and a maternal imprinted gene that functions during central cell, embryo and endosperm development. Seeds that develop from mea mutant egg cells abort regardless of the paternal genotype. With this approach, we aim to uncover putative genes that are downstream of MEA and might cause the seed abortion phenotype. For this, we compare three developmental time point datasets between wild-type and mea mutant: ovary (before fertilization), and seed at 1-2 and 4 days after pollination (DAP).

2021-06-25 | E-MTAB-9569 | biostudies-arrayexpress

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Project description:The goal of this analysis is to compare the transcriptome profile (RNA-seq) along different developmental ages in the naked mole rat ovary

2023-02-21 | GSE139515 | GEO

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Project description:Flowers have a species-specific fertile period during which pollination and fertilization have to occur to initiate seed and fruit development. Within the flower, the functional life span of the ovule containing the female gametophyte is decisive for fertilization and the initiation of seed development. Here we performed an RNA-sequencing based transcriptome analysis of senescing unfertilized ovules during in a time series. We isolated ovules from Arabidopsis thaliana flowers emasculated at stage 12c at three different time points: 2 days after emasculation (DAE), 3 DAE, and 4 DAE. These time points correspond to intact mature ovules (2DAE), early ovule senescence (3 DAE), and late ovule senescence (4 DAE). We extracted total RNA from the ovules in 3 independent biological replicates, thus generating 9 RNA samples in total, for RNA-sequencing by Illumina HiSeq.

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A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

Project description:Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.

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Project description:The expression levels of Arabidopsis thaliana (Col-0) genes in several developmental stages during the seed-to-seedling transition were measured by using high-density Affymetrix® arrays (Aragene.st1.1). We used a time-series of microarrays to gain temporal resolution and identify relevant genes in the seed-to-seedling transition.

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Gene expression profiling via LongSAGE in a non-model plant species: A case study in seeds of Brassica napus

Project description:Serial Analysis of Gene Expression (LongSAGE) was applied for gene expression profiling in seeds of oilseed rape (Brassica napus ssp. napus). The usefulness of this technique for detailed expression profiling in a non-model organism was demonstrated for the highly complex, neither fully sequenced nor annotated genome of B. napus by applying a tag-to-gene matching strategy based on Brassica ESTs and the annotated proteome of the closely related model crucifer A. thaliana. Transcripts from 3,094 genes were detected at two time-points of seed development, 23 days and 35 days after pollination (DAP). Differential expression in about 10 % of all matched genes, with a total abundance of 44 %, showed a shift from gene expression involved in diverse developmental processes including cell proliferation and seed coat formation at 23 DAP to more focussed metabolic processes including storage protein accumulation and lipid deposition at 35 DAP. The most abundant transcripts at 23 DAP were coding for diverse protease inhibitor proteins and proteases, including cysteine proteases involved in seed coat formation and a number of lipid transfer proteins involved in embryo pattern formation. At 35 DAP, transcripts encoding napin, cruciferin and oleosin storage proteins were most abundant. Over both time-points, 18.6 % of A. thaliana genes were matched by Brassica ESTs detected by LongSAGE tags in antisense orientation. This suggests a strong involvement of antisense transcript expression in regulatory processes during B. napus seed development.

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