Transcriptome analysis of Arabidopsis siliques
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB25745 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lysine 2-hydroxyisobutyrylation (Khib) is one of the newly discovered post-translational modifications (PTMs) through protein acylation. It has been reported to be widely distribute in both eukaryotes and prokaryotes, and plays an important role in chromatin conformation change, gene transcription, subcellular localization, protein-protein interaction, signal transduction, and cellular proliferation. In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that this highly conserved modification was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: 3810 normalized 2-hydroxyisobutyrylation sites on 1254 proteins were identified in siliques under salt stress, and lysine 2-hydroxyisobutyrylation was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism. Overall, our work reveals the first systematic analysis of Khib proteome in Arabidopsis siliques under salt stress, and sheds a light on the future studies on the regulatory mechanisms of Khib during the salt stress response of plants.
2021-12-30 | PXD026643 | Pride
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2016-03-28 | E-GEOD-55866 | biostudies-arrayexpress
Project description:To search for the differential expressed genes during postferlization and embryonic development in Arabidopsis, We profiled transcriptome of siliques at 4 developmental stages using RNA-seq based on poly(A) selection. Each RNA library yielded 100 million 101-bp paired-end reads.Using Tophat and Cufflinks with the Arabidopsis TAIR10 annotation as reference, we identifed 33,451 assembled transcripts in 4 samples. Of them, 5,608 were up-regulated genes in at least one sample. A group of them are preferentially expressed at mature green-stage of seeds.
2016-03-28 | GSE55866 | GEO
Project description:Pollen is the male gametophyte of land plants. Proper development and maturation of pollen is necessary for the successful reproduction of seed plants. This process involves sophisticated coordination between sporophytic and gametophytic tissues in anthers. To advance the mechanistic studies of anther development, additional players need to be discovered for a comprehensive understanding of the underlying regulatory network. Here we show that the Arabidopsis dual specificity tyrosine phophorylated and regulated kinase (DRYK), AtYAK1, is essential for development of rosette leaves and the male but not female gametophyte in Arabidopsis. Arabidopsis mutant plants carrying a mutation in AtYAK1 produce developmentally stalled microspores, likely because of the defects in the two consecutive mitosis steps in the post-meiotic maturation process of pollen. The mutation of AtYAK1 has a significant effect on gene expression programs in developing pollen. Transcritpome analysis of atyak1 revealed downstream genes in families of protein kinases, transporters and transcription factors, which potentially contribute to pollen development. This study represents the first molecular characterization of DYRK in the plant kingdom. Our results also imply that the regulation of cytokinesis by DYRKs is evolutionally conserved in fungus, fruit fly, animals and plants. 2 biological replicates were performed for wt and 2 different alleles of ayak1 mutants (atyak1-1 and atyak1-2)
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Project description:Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana siliques. m5C sites were also analyzed in an Arabidopsis T-DNA knockout for the RNA methyltransferase TRM4B.
2017-04-07 | GSE80050 | GEO
Project description:Pollen is the male gametophyte of land plants. Proper development and maturation of pollen is necessary for the successful reproduction of seed plants. This process involves sophisticated coordination between sporophytic and gametophytic tissues in anthers. To advance the mechanistic studies of anther development, additional players need to be discovered for a comprehensive understanding of the underlying regulatory network. Here we show that the Arabidopsis dual specificity tyrosine phophorylated and regulated kinase (DRYK), AtYAK1, is essential for development of rosette leaves and the male but not female gametophyte in Arabidopsis. Arabidopsis mutant plants carrying a mutation in AtYAK1 produce developmentally stalled microspores, likely because of the defects in the two consecutive mitosis steps in the post-meiotic maturation process of pollen. The mutation of AtYAK1 has a significant effect on gene expression programs in developing pollen. Transcritpome analysis of atyak1 revealed downstream genes in families of protein kinases, transporters and transcription factors, which potentially contribute to pollen development. This study represents the first molecular characterization of DYRK in the plant kingdom. Our results also imply that the regulation of cytokinesis by DYRKs is evolutionally conserved in fungus, fruit fly, animals and plants.
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2013-12-23 | E-GEOD-49950 | biostudies-arrayexpress