Single-cell transcriptomic analysis of rice root tips [bulk RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA609101 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11194109_1.fastq.gz | Fastqsanger.gz | |||
| SRR11194109_2.fastq.gz | Fastqsanger.gz | |||
| SRR11194110_1.fastq.gz | Fastqsanger.gz | |||
| SRR11194110_2.fastq.gz | Fastqsanger.gz | |||
| SRR11194111_1.fastq.gz | Fastqsanger.gz |
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Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
2020-12-25 | GSE146033 | GEO
Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.
2020-12-25 | GSE146034 | GEO
Project description:Single-cell transcriptomic analysis of rice root tips
| PRJNA609092 | ENA
Project description:The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer. Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer. Keywords: Genotype comparison, root impedance response
2008-03-19 | GSE10857 | GEO
Project description:Single-cell transcriptomic analysis of rice root tips [scRNA-seq]
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Project description:Gene expression profile of response to auxin at 3 h after treatment in rice root tips: IR64 (loss-of-function of DRO1 type) vs Near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL; gain-of-function of DRO1 type) We used two rice varieties, IR64 and near-isogenic line homozygous for the Kinandang Patong allele of DRO1 in an IR64 genetic background (Dro1-NIL). We performed comprehensive microarray analysis of rice root tips with auxin treatment (3h) and pre-treatment (0h) in IR64 and Dro1-NIL. Seedling root tips of IR64 and Dro1-NIL were treated with 10 M-BM-5M 2,4-D. n = 3 biological repeats (15 seedlings per repeat).
2013-05-07 | E-GEOD-46255 | biostudies-arrayexpress
Project description:Background: Single-cell reconstruction of gene regulatory programs provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While the single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes remain largely unknown. Results: To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell-type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin dynamics and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat, and identify cell type specific accessibility changes to this key environmental stimulus. Conclusions: Our work provides a framework for the integrative analysis of regulatory dynamics in an important plant organ at single-cell resolution.
2022-11-17 | GSE214131 | GEO
Project description:Background: Single-cell reconstruction of gene regulatory programs provides an important tool to understand the cellular phenotypic variation in complex tissues and their response to endogenous and environmental stimuli. While the single-cell transcriptomes of several plant organs have been elucidated, the underlying chromatin landscapes remain largely unknown. Results: To comprehensively delineate chromatin accessibility during root development of an important crop, we applied single-cell ATAC-seq to 46,758 cells from rice root tips under normal and heat stress conditions. Our data revealed cell-type-specific accessibility variance across most of the major cell types and allowed us to identify sets of transcription factors which associate with accessible chromatin regions (ACRs). Using root hair differentiation as a model, we demonstrate that chromatin dynamics and gene expression dynamics during cell type differentiation correlate in pseudotime analyses. In addition to developmental trajectories, we describe chromatin responses to heat, and identify cell type specific accessibility changes to this key environmental stimulus. Conclusions: Our work provides a framework for the integrative analysis of regulatory dynamics in an important plant organ at single-cell resolution.
2022-11-17 | GSE214130 | GEO
Project description:We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones. For each section, we include 6 biological replicates. We also include the whole-root samples that include all developmental zones. The genes with enriched expression in certain developmental zones were used as developmental stage markers for our following single-cell RNA sequencing annotation.
2024-07-01 | E-MTAB-13889 | biostudies-arrayexpress
Project description:We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones
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