Transcriptome analysis of ATG-silenced pollen
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA667028 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12764487_1.fastq.gz | Fastqsanger.gz | |||
| SRR12764487_2.fastq.gz | Fastqsanger.gz | |||
| SRR12764488.fastq.gz | Fastqsanger.gz | |||
| SRR12764489.fastq.gz | Fastqsanger.gz | |||
| SRR12764490.fastq.gz | Fastqsanger.gz |
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Project description:The goal of present study aimed to investigate the impact of downregulation of ATG2 and ATG5 on pollen transcriptome.
2023-10-23 | GSE158922 | GEO
Project description:Pollen tubes extend through pistil tissues and are guided to ovules where they release sperm for fertilization. Although pollen tubes can germinate and elongate in a synthetic medium, their trajectory is random and their growth rates are slower compared to growth in pistil tissues. Furthermore, interaction with the pistil renders pollen tubes competent to respond to guidance cues secreted by specialized cells within the ovule. The molecular basis for this potentiation of the pollen tube by the pistil remains uncharacterized. We used a surgical procedure to obtain large quantities of uncontaminated pollen tubes that grew through the pistil and defined their transcriptome by microarray analysis. We also characterized the transcriptome of in vitro-grown pollen tubes (for 0.5hours or 4hours) and dessicated mature pollen in Arabidopsis.
2009-07-28 | GSE17343 | GEO
Project description:Transcriptome analysis of heat stressed Nicotiana tabacum pollen tubes
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Project description:Pollen development is central for plant reproduction and is assisted by changes of the transcriptome and the proteome. At the same time, pollen is largely heat sensitive, particularly at early developmental stages. To define the changes during development and the response of different stages to elevated temperatures we investigated the transcriptome and proteome of pollen at tetrad, post-meiotic and mature stage before and after application of elevated temperatures. We used Solanum lycopersicum as an economically important crop. We demonstrate that the number of transcripts declines from tetrad to mature stage, while the protein content shows the opposite trend. Comparison of the transcriptome and proteome led to the discovery of two translational modes assigned as direct translation – transcripts increased in a specific pollen stage lead to increased translation in the same stage – and delayed translation – transcripts are produced for translation in later stages. The response to elevated temperatures is with ~5% of all genes being upregulated comparable to general plant behavior. The alteration at proteome level marked the mature pollen as least responsive and the post-meiotic stages as most responsive with altered levels of 40% of the identified proteins. For a subset of the genes with direct translation we observed a downregulation of protein levels after heat stress, whereas some of the genes with delayed translation showed a shift from delayed to direct translation when heat stress is applied. Further, Hsps, proteasome subunits, ribosomal proteins as well as eukaryotic initiation factors are the most drastically affected groups. On the example of Hsps we document that the response at transcriptome and proteome levels in e.g. the post-meiotic and mature stage does not correlate. Moreover, while all stages respond to heat stress with regulation of transcript abundance of Hsps in a comparable manner, changes at proteome level are distinct. Thus, we demonstrate that the difference in heat stress response in different stages of pollen development is rather manifested by significant changes of protein than transcript abundance.
2015-05-15 | PXD008762 | Pride
Project description:In flowering plants, pollen development is under a dynamic and well-orchestrated transcriptional control, characterized by an early phase with high transcript diversity and a late post-mitotic phase skewed to a cell-type specific-transcriptome. Such transcriptional changes require a balance between synthesis and degradation of mRNA transcripts, the latter being initiated by deadenylation. The CCR4-NOT complex is the main evolutionary conserved deadenylase complex in eukaryotes, and its function is essential during germline specification in animals. We hypothesised that the CCR4-NOT complex might play a central role in mRNA turnover during microgametogenesis in Arabidopsis. Disruption of NOT1 gene, which encodes the scaffold protein of the CCR4-NOT complex, showed abnormal seed set. Genetic analysis failed to recover homozygous progeny and reciprocal crosses confirmed reduced transmission through the male and female gametophytes. Concordantly not1 embryo sacs showed delayed development and defects in embryogenesis. not1 pollen grains exhibited abnormal male germ unit configurations and failed to germinate. Transcriptome analysis of pollen from not1/+ mutants revealed that lack of NOT1 leads to an extensive transcriptional deregulation during microgametogenesis. Therefore, our work establishes NOT1 as an important player during gametophyte development in Arabidopsis.
2020-04-24 | GSE133490 | GEO
Project description:We isolated tricellular pollen (TCP) and pollen mother cells (PMC) of rice using laser microdissection, and did microarray analysis with Agilent 44k rice array.
2010-07-31 | GSE17098 | GEO
Project description:Pollen tubes extend through pistil tissues and are guided to ovules where they release sperm for fertilization. Although pollen tubes can germinate and elongate in a synthetic medium, their trajectory is random and their growth rates are slower compared to growth in pistil tissues. Furthermore, interaction with the pistil renders pollen tubes competent to respond to guidance cues secreted by specialized cells within the ovule. The molecular basis for this potentiation of the pollen tube by the pistil remains uncharacterized. We used a surgical procedure to obtain large quantities of uncontaminated pollen tubes that grew through the pistil and defined their transcriptome by microarray analysis. We also characterized the transcriptome of in vitro-grown pollen tubes (for 0.5hours or 4hours) and dessicated mature pollen in Arabidopsis. Experiment Overall Design: Pollen and pollen tubes were collected as described in the protocols section for RNA extraction and hybridization on Affymetrix ATH1 Genechip microarrays.
2009-08-15 | E-GEOD-17343 | biostudies-arrayexpress
Project description:Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant Arabidopsis thaliana, which has tri-cellular pollen grains at maturity. Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip® to perform transcriptional profiling on mature bi-cellular soybean pollen. Results: Compared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean unique transcripts addressed in this study, 10,299 genes (27.46%) are expressed in pollen. Of the pollen-expressed genes, about 9,489 (92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), cell cycle-related transcripts, signal recognition receptors, ethylene responsive factors, chromatin remodeling factors, and members of the ubiquitin proteasome proteolytic pathway. Moreover, we identify several new pollen-specific candidate genes that might play a significant role in pollen biology. Conclusion: This is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. We also demonstrate that pollen is a rich store of regulatory proteins that are essential and sufficient for de novo gene expression. A comparison between transcription factors up-regulated in soybean and those upregulated in Arabidopsis revealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.
2009-03-26 | GSE12286 | GEO
Project description:In this study, we investigated the differential metabolic pathway enrichment among mature, hydrated, and germinated pollen using untargeted metabolomics analysis. Integration of publicly available transcriptome with presented metabolome data revealed starch and sucrose metabolism was significantly increased during pollen hydration and germination. The alterations in central metabolism focusing on sugar, fatty acids, and lipids were analyzed in detail. Several metabolites, including palmitic acid, oleic acid, linolenic acid, quercetin, luteolin/kaempferol, and γ-aminobutyric acid (GABA), were elevated in the hydrated pollen, suggesting a potential role in activating pollen tube emergence. The metabolite levels of mature, hydrated, and germinated pollen, presented in this work provide insights on the molecular basis of pollen germination.
2022-01-17 | ST002060 | MetabolomicsWorkbench
Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups.
2013-02-28 | GSE37157 | GEO