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E-CURD-28

ABSTRACT: Diversification of Root Hair Development Genes in Vascular Plants - rice dataset

PROVIDER: E-CURD-28 | ExpressionAtlas | 2020-04-03

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-CURD-28-analysis-methods.tsv	Tabular
	E-CURD-28-analytics.tsv	Tabular
	E-CURD-28-atlasExperimentSummary.Rdata	Rdata
	E-CURD-28-configuration.xml	Xml
	E-CURD-28-g2_g1-mvaPlot.png	Other

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E-CURD-29

Project description:Diversification of Root Hair Development Genes in Vascular Plants - arabidopsis thaliana dataset

2020-04-03 | E-CURD-29 | ExpressionAtlas

Diversification of Root Hair Development Genes in Vascular Plants

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

Diversification of Root Hair Development Genes in Vascular Plants

Project description:Diversification of Root Hair Development Genes in Vascular Plants

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Single-cell transcriptomic analysis of rice root tips [bulk RNA-seq]

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

Single-cell transcriptomic analysis of rice root tips [scRNA-seq]

2020-12-25 | GSE146034 | GEO

MERISTEM ACTIVITYLESS1 (MAL1) is involved in crown root development through the maintenance of meristem size in rice

Project description:Rice MERISTEM ACTIVITYLESS1 (MAL1) is an RING-H2 finger domain (RFD) contained gene. To elucidate the molecular functions of MAL1 during crown root development, we generated MAL1 knock-down transgenic plants. MAL1 RNA interfering (RNAi) transgenic plants exhibited shorter crown root length and less crown root number phenotype accompanied by low cell division rate.Here we sought to find the downstream genes of OsMAL1 in rice crown root tip

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root hair-expressed genes in rice

Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar

2018-03-03 | GSE111350 | GEO

Root hair-expressed genes in rice

Project description:To identifiy root hair-preferred genes in rice, we perform microarray using root hairs sample from don-gin and lon-gin cultivar

2018-01-30 | GSE109811 | GEO

root hair-expressed genes in rice

Project description:root hair-expressed genes in rice

| PRJNA436704 | ENA

Root hair-expressed genes in rice

Project description:Root hair-expressed genes in rice

| PRJNA432070 | ENA