E-MTAB-11005
Ontology highlight
ABSTRACT:
TISSUE(S): Leaf Collar, Leaf Sheath, Root Hair, Anther Wall, Ligule
PROVIDER: E-MTAB-11005 | ExpressionAtlas | 2023-06-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-11005-analysis-methods.tsv | Tabular | |||
| E-MTAB-11005-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-11005-coexpressions.tsv.gz | Tabular | |||
| E-MTAB-11005-configuration.xml | Xml | |||
| E-MTAB-11005-factors.xml | Xml |
Items per page: 5 1 - 5 of 32 |
Similar Datasets
Project description:RNA-Seq of various rice tissues (Root hair, Collar, Leaf sheath, Ligule, Anther wall)
| PRJEB47919 | ENA
Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.
2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109617 | GEO
Project description:To elucidate the epigenetic regulation of salt-responsive genes helps to understand the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms function in regulating the salt-responsive genes in rice and other crops at a global level. In this study, we mainly focused on dynamic changes in transcriptome and histone marks between rice leaf and root tissues during salt treatment by using RNA-seq and ChIP-seq approaches. We demonstrated that the majority of salt-related differentially expressed genes (DEGs) display tissue-dependent changes. Similarly, tissue-dependent chromatin changes have been detected between leaf and root tissues during salt treatment. Most importantly, our study indicates that chromatin states with a combination of marks, rather than an individual mark, most likely play crucial roles in regulating differential expression of salt-responsive genes between leaf and root tissues. Especially, a special CS containing bivalent marks, H3K4me3 and H3K27me3 with a functional exclusion with each other, displays distinct functions in regulating expression of DEGs between leaf and root tissues, H3K27me3-related repressive mark mainly regulates expression of DEGs in root, but H3K4me3-releated active mark dominantly functions in regulation of down-regulated genes and possibly antagonize the repressive role of H3K27me3 in up-regulated genes in leaf. Thus, our findings indicate salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice, which provides new insights in the understanding of chromatin-based epigenetic mechanisms that confer salt tolerance in plants.
2019-06-19 | GSE109616 | GEO
Project description:The RNA-seq data was generated to identify the genes that are expressed in rice leaf sheath
2020-03-01 | E-MTAB-8353 | biostudies-arrayexpress
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:Purpose: The root hair is a model for understanding evolution of individual cell differentiation programs in plants. We compare the expression of the genes that participate in root hair development between Arabidopsis and other vascular plants to assess the conservation/diversification of the root hair development programs in vascular plants. Methods: We used RNA-Seq, in triplicates, to measure the genome-wide transcription activity of the root-hair cells isolated by Fluorescence-activated cell sorting (FACS) in Arabidopsis (COBL9::GFP transgeneic line, AtRH) and rice (EXPA30::GFP transgenic line, OsRH). We also generated RNA-Seq data, in triplicates, on the Arabidopsis rhd6 WER::GFP and WT WER::GFP by FACS to identify the RHD6-regulating root hair morphogenesis genes (AtRHM). For Arabidopsis, rice, tomato, soybean, cucumber and maize, we used RNA-seq, in triplicates, to measure genome-wide transcription activity of root hair cells filtered by sieves after stirred in liquid nitrogen (HAIR genes). Each sample was trimmed to retain high-quality reads, mapped to the reference genome by TopHat, and quantified by Cufflinks. The number of raw reads of Arabidopsis rhd6 WER::GFP and WT WER::GFP sample was counted by HTSeq and analyzed by edgeR to identify the differentially expressed genes. Results: We defined the root-hair transcriptome in diverse vascular plant species and analyzed the relative conservation/divergence in the expression of a large set of gene families.
2017-05-11 | GSE85516 | GEO
Project description:Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages.
2020-10-06 | GSE159047 | GEO
Project description:Insufficient leaf photosynthesis promotes sheath NSC transport to the panicle during grain filling. SnRK1 regulates assimilate distribution between plant tissues and organs. However, the mechanism by which SnRK1 regulates sheath NSC transport to the panicle and its response to limited leaf assimilation remain unclear. Here, we performed leaf cutting (LC) at anthesis to simulate insufficient leaf assimilation and set no treatment as a CK. In response to LC, SnRK1 activity increased rapidly, and NSC transport was advanced. Sheath NSCs were not transported in a snrk1a mutant with deficient SnRK1 activity. These results indicated that SnRK1 activity is important for sheath NSC transport. The high correlation of T6P and sucrose and the inhibition of SnRK1 by T6P in sheaths in vitro implied that T6P slightly inhibits SnRK1 activity in rice sheaths in response to sucrose availability. The increase in SnRK1 activity was accompanied by an increase in OsSnRK1a expression and a low sucrose content. Low sucrose signaling increases SnRK1 transcription. Therefore, we speculated that OsSnRK1a expression positively regulates SnRK1 activity in response to low sucrose availability in rice sheaths. Through phosphoproteomics and further PRM verification, 20 phosphosites that depend on SnRK1 and are correlated with NSC transport were obtained. Based on the function of these sites and proteins, we found that SnRK1 regulates starch degradation, sucrose metabolism, phloem transport, sugar transport across tonoplast, and glycolysis via phosphorylation to promote sheath NSC transport. Overall, our results revealed the importance, function and regulatory mechanism of SnRK1 in sheath NSC transport.
2022-03-18 | PXD024675 | Pride
Project description:Insufficient leaf photosynthesis promotes sheath NSC transport to the panicle during grain filling. SnRK1 regulates assimilate distribution between plant tissues and organs. However, the mechanism by which SnRK1 regulates sheath NSC transport to the panicle and its response to limited leaf assimilation remain unclear. Here, we performed leaf cutting (LC) at anthesis to simulate insufficient leaf assimilation and set no treatment as a CK. In response to LC, SnRK1 activity increased rapidly, and NSC transport was advanced. Sheath NSCs were not transported in a snrk1a mutant with deficient SnRK1 activity. These results indicated that SnRK1 activity is important for sheath NSC transport. The high correlation of T6P and sucrose and the inhibition of SnRK1 by T6P in sheaths in vitro implied that T6P slightly inhibits SnRK1 activity in rice sheaths in response to sucrose availability. The increase in SnRK1 activity was accompanied by an increase in OsSnRK1a expression and a low sucrose content. Low sucrose signaling increases SnRK1 transcription. Therefore, we speculated that OsSnRK1a expression positively regulates SnRK1 activity in response to low sucrose availability in rice sheaths. Through phosphoproteomics and further PRM verification, 20 phosphosites that depend on SnRK1 and are correlated with NSC transport were obtained. Based on the function of these sites and proteins, we found that SnRK1 regulates starch degradation, sucrose metabolism, phloem transport, sugar transport across tonoplast, and glycolysis via phosphorylation to promote sheath NSC transport. Overall, our results revealed the importance, function and regulatory mechanism of SnRK1 in sheath NSC transport.
2022-03-18 | PXD024670 | Pride