Ontology highlight
ABSTRACT:
PROVIDER: PRJNA974895 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24682242_1.fastq.gz | Fastqsanger.gz | |||
| SRR24682242_2.fastq.gz | Fastqsanger.gz | |||
| SRR24682243_1.fastq.gz | Fastqsanger.gz | |||
| SRR24682243_2.fastq.gz | Fastqsanger.gz | |||
| SRR24682244_1.fastq.gz | Fastqsanger.gz |
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Project description:Somatic embryogenesis is an important biological process in several plant species, including sugarcane. Proteomics approaches have shown that H+ pumps are differentially regulated during somatic embryogenesis; however, the relationship between H+ flux and embryogenic competence is still unclear. This work aimed to elucidate the association between extracellular H+ flux and somatic embryo maturation in sugarcane. We performed a microsomal proteomics analysis and analyzed changes in extracellular H+ flux and H+ pump (P-H+-ATPase, V-H+-ATPase and H+-PPase) activity in embryogenic and non-embryogenic callus. A total of 657 proteins were identified, 16 of which were H+ pumps. We observed that P-H+-ATPase and H+-PPase were more abundant in embryogenic callus. Compared with non-embryogenic callus, embryogenic callus showed high H+ influx, especially at maturation day 14 as well as higher H+ pump activity, mainly P-H+-ATPase and H+-PPase activity. The H+-PPase appears to be the major H+ pump in embryogenic callus during somatic embryo formation, functioning in both vacuole acidification and PPi homeostasis. These results provide evidence for an association between higher H+ pump protein abundance and, consequently, higher H+ flux and embryogenic competence acquisition in the callus of sugarcane.
2018-06-26 | PXD009858 | Pride
Project description:Histone modification H3K27me3 profilings by the CUT&RUN method (Skene et al., 2017) were performed using embryonic callus and non-embryonic callus of Picea abies to identify genes related to somatic embryogenesis capacity.
2020-08-01 | GSE145331 | GEO
Project description:Transcriptome analysis of small RNA was performed using pollen and embryonic callus, and vegetative tissues, needles of Picea abies to address differences in small RNA profiles between reproductive tissues and vegetative tissues in gymnosperm.
2019-12-21 | GSE129413 | GEO
Project description:Purpose: Maize somatic embryogenesis is usually required to achieve genetic transformation and represents an important alternative in plant development. Although many embryogenesis-related genes have been studied in this model, the molecular mechanisms underlying cell dedifferentiation and further plant regeneration are not completely understood. Methods: Immature embryos smRNA profiles of 15-day-after-pollination (IE) and Embryogenic Callus from one (C1), four (C4), and ten months (C10) were generated by deep sequencing, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed with two methods: Bowtie 1.1.2 and ShortStack 3.4. qRT–PCR validation for selected miRNAs was performed using SYBR Green assays. Results: We used high throughput sequencing to explore the sRNA populations during maize embryogenic callus induction and established subcultures from the Mexican cultivar VS-535, Tuxpeño landrace. We detected readjustments in 24 nt and 21-22 nt sRNA populations during the embryogenic callus establishment and maintenance. miRNAs related to stress response substantially increased upon callus proliferation establishment, correlating with a reduction in some of their target levels. On the other hand, while 24 nt-long hc-siRNAs derived from transposable retroelements transiently decreased in abundance during the embryogenic callus establishment, a population of 22 nt- hc-siRNAs increased. This was accompanied by reduction in transposon expression in the established callus subcultures. Conclusions: Stress- and development-related miRNAs are highly expressed upon maize EC callus induction and during maintenance subcultures, while miRNAs involved in hormone response only transiently increase during induction. The establishment of proliferative maize embryogenic callus is accompanied by important readjustments in the length of hc-siRNAs mapping to LTR retrotransposons, and their expression regulation.
2020-04-21 | GSE98055 | GEO
Project description:gnp07_regeneome_embryogenesis - embryogenesis col0 - Identify genes involved in somatic embryogenesis - compare embryogenic areas of a callus with undifferenciate area in the same callus
2012-06-01 | GSE30425 | GEO
Project description:gnp07_regeneome_embryogenesis - embryogenesis ws - Identify genes involved in somatic embryogenesis - To compare embryogenic areas of a callus with undifferenciate area in the same callus
2012-06-01 | GSE30383 | GEO
Project description:Objectives: to characterize and to better understand differences at a protein level in embryonic and non-embryogenic tissues of embryonal masses in Douglas-fir. In Europe, Douglas-fir is a major species for reforestation with increasing demand for its wood. Harvested stems provide timber of outstanding wood quality, mechanical properties and durability. Commercial Douglas-fir plantations in France are limited by the ability to produce seed from the latest breeding developments. Somatic embryogenesis is considered a promising biotechnology for large-scale clonal propagation of forest trees, due to the high multiplication rates it can provide. Moreover, embryogenic cultures are amenable to both cryogenic storage for long-term preservation of genetic resources and genetic engineering (including genome editing) for functional characterization of genes expressed during embryogenesis. In conifers, embryogenic cultures take the form of embryonal mass made up of early differentiated cells forming immature somatic embryos that proliferate via cleavage polyembryony. In Douglas-fir embryogenic lines consisting in embryonal mass have been compared to non-embryogenic callus during their proliferation. Comparison of proteomes (free-gel proteomics) of embryonal mass vs non-embryogenic callus were performed.
2019-05-17 | PXD011176 | Pride
Project description:gnp07_regeneome_embryogenesis - embryogenesis col0 - Identify genes involved in somatic embryogenesis - compare embryogenic areas of a callus with undifferenciate area in the same callus 4 dye-swap - tissue comparison
2012-05-31 | E-GEOD-30425 | biostudies-arrayexpress
Project description:The cost of Carica papaya production through seed-based propagation is increased by sex segregation, making in vitro techniques a more appealing option for clonal propagation. Inducing embryogenic callus with 2,4-dichlorophenoxyacetic acid (2,4-D) hold the potential to large-scale cloning, although the molecular mechanisms underlying this process are still not well understood. In this study, we performed a temporal analysis in the proteome of C. papaya callus to identify the key players involved in embryogenic differentiation. Mature zygotic embryos were used as explants and treated with 20 μM 2,4-D to induce embryogenic callus. Total proteins were extracted at 0, 7, 14, and 21 days (T0, T7, T14, and T21), and 1407 proteins were identified using bottom-up proteomic approach. Comparative proteomics revealed 957 differentially accumulated proteins (DAPs) (p<0.05 and log2FC >0.585 or <-0.585) in at least one comparison between the analyzed induction times points. The clustering analysis revealed four clusters with distinct patterns of protein accumulation throughout the embryogenic callus induction treatment. The cluster 1 contains 386 DAPs that accumulated at all analyzed times after treatment with 2,4-D. In contrast, cluster 2 contains 165 DAPs that decrease in abundance during the induction. The cluster 3 contains 251 proteins that are most abundant just after the start of incubation in 2,4-D (T7) and cluster 4 grouped 155 proteins that accumulate after callus formation. Functional analysis revealed that proteins involved with reserve storage and seed maturation were more abundant in the explant at T0 and decreased as callus formation progressed. Biological processes involving carbohydrate and amino acid metabolism, aerobic respiration, and protein catabolic processes were enriched after induction treatment. Regulatory proteins, including histone deacetylase (HDT3) and argonaute 1, were more abundant after the start of induction treatment with 2,4-D, suggesting their role in acquisition of embryogenic competence. Predicted protein-protein networks revealed the regulatory role of proteins 14.3.3 accumulated during callus induction and the association of proteins involved in oxidative phosphorylation, hormone response, and SAM metabolism. Our findings emphasize the modulation of the proteome at different stages during embryogenic callus initiation and identify regulatory proteins that might be involved with the activation of this process.
2024-01-26 | PXD046521 | Pride