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Root sample

ABSTRACT: root sample Raw sequence reads

PROVIDER: PRJNA550311 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR9595670_1.fastq.gz	Fastqsanger.gz
	SRR9595670_2.fastq.gz	Fastqsanger.gz
	SRR9595671_1.fastq.gz	Fastqsanger.gz
	SRR9595671_2.fastq.gz	Fastqsanger.gz
	SRR9595672_1.fastq.gz	Fastqsanger.gz

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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