A single-cell multiomics atlas of rice organs
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA974167 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24653525_1.fastq.gz | Fastqsanger.gz | |||
| SRR24653525_2.fastq.gz | Fastqsanger.gz | |||
| SRR24653526_1.fastq.gz | Fastqsanger.gz | |||
| SRR24653526_2.fastq.gz | Fastqsanger.gz | |||
| SRR24653527_1.fastq.gz | Fastqsanger.gz |
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Project description:Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the world’s major crop plants. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs we were able to identify cell-type specific gene regulatory networks and describe novel cell states, such as the “transition status” in floral meristems during panicle development. Based on our network analyses we uncovered the function of cell type-specific regulatory hubs RSR1, F3H and LTPL120 for rice development. Importantly, our analysis revealed a correlation between cell type and agronomic traits, and conserved and divergent cell type functions during evolution. In summary, this study not only offers a valuable single-cell multiomics resource for a major crop, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.
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Project description:Cell functions across eucaryotes are driven by specific gene expression programs that are dependent on chromatin structure. Here, we report a single-cell multiomics atlas of rice, one of the world’s major crop plants. By simultaneously profiling chromatin accessibility and RNA expression in 116,564 cells from eight organs we were able to identify cell-type specific gene regulatory networks and describe novel cell states, such as the “transition status” in floral meristems during panicle development. Based on our network analyses we uncovered the function of cell type-specific regulatory hubs RSR1, F3H and LTPL120 for rice development. Importantly, our analysis revealed a correlation between cell type and agronomic traits, and conserved and divergent cell type functions during evolution. In summary, this study not only offers a valuable single-cell multiomics resource for a major crop, but also enriches our understanding of the intricate roles and molecular underpinnings of individual cell types in rice.
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Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. This SuperSeries is composed of the following subset Series: GSE13988: Rice expression atlas (1): Anther development GSE14298: Rice expression atlas (2): Pollination - Fertilization GSE14299: Rice expression atlas (3): Early embryogenesis GSE14300: Rice expression atlas (4): Vegetative tissues GSE14301: Rice expression atlas (5): Anther development (Agilent data) Refer to individual Series
2010-11-11 | E-GEOD-14304 | biostudies-arrayexpress
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2015-11-25 | E-GEOD-56463 | biostudies-arrayexpress
Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison, platform comparison Anther development of rice from hypodermal archesporial cells formation to tri-cellular mature pollens were divided into eight stages. Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 26.
2010-11-11 | E-GEOD-13988 | biostudies-arrayexpress
Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison, time course 0-4 DAP embryosacs were collected, and dissected into bottom 1/4 part (contains embryo) and remaining top 3/4 part (mainly endosperm). Two or three biological replicates for each tissue-stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 27. Unpollinated embryo and ovary samples were references in this series.
2010-11-11 | E-GEOD-14299 | biostudies-arrayexpress
Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison, time course Pollinating pistils were collected according to time after pollination. Unpollinatted pistils and pistils 5 min after pollination were separated into stigmas and ovaries. Two or three biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 20. Unpollinated samples were references in this series.
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Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison Regenerating calli on agar plate, young leaves and roots grown in a green house, shoots grown in growth chamber were collected as references of reproductive samples. Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 25.
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