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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

ABSTRACT: An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

PROVIDER: PRJNA757403 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15598392_1.fastq.gz	Fastqsanger.gz
	SRR15598392_2.fastq.gz	Fastqsanger.gz
	SRR15598393_1.fastq.gz	Fastqsanger.gz
	SRR15598393_2.fastq.gz	Fastqsanger.gz
	SRR15598394_1.fastq.gz	Fastqsanger.gz

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

Project description:An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]

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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]

Project description:Single cell sequencing has recently allowed the generation of exhaustive root cell atlases. However, some cell types are elusive and remain underrepresented. Here, we use a second-generation single cell approach, where we zoom in on the root transcriptome by sorting cells with specific markers, to profile the phloem poles at an unprecedented resolution. Our data highlight the similarities among the developmental trajectories and gene regulatory networks communal to protophloem sieve element (PSE) adjacent lineages in relation to PSE enucleation, a key event in phloem biology. As a signature for early PSE-adjacent lineages, we have identified a set of DNA-binding with one finger (DOF) transcription factors, the PINEAPPLEs (PAPL), that act downstream of PHLOEM EARLY DOF (PEAR) genes, and are important to guarantee a proper root nutrition in the transition to autotrophy. Our data provide a holistic view of the phloem poles that act as a functional unit in root development.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description:This sudy focuses on the identification of transcripts in the shoot phloem of the model plant Arabidopsis thaliana. Transcripts expressed in the phloem tissue (parenchyma cell, companion cell, sieve element) were excised by laser microdissection pressure catapulting (LMPC). These were compared with transcripts isolated from leaf phloem exudates by EDTA-chelation technique. Optimization of sample harvest resulted in RNA of high quality from both sources. Modifications of the RNA amplification procedure obtained RNA of sufficient yield and quality for microarray experiments. Microarrays (Affymetrix, ATH1) hybridized with RNA derived from phloem tissue by LMPC or phloem sap allowed us to differentiate between phloem located and mobile transcript species. The datasets provide a search criterion for phloem-based signals and will facilitate reverse genetic studies and forward genetic screens for phloem and long distance RNA signaling mutants. Experiment Overall Design: Arabidopsis plants were cultivated under short day conditions (8 h light) until flowering. Phloem tissue was isolated by Lasermicrodissection and Pressure Catapulting (LMPC) and phloem exudate by EDTA-chelation technique. In both experiments poly-A-RNA was extracted and amplified before hybridization of microarrays (Affymetrix, ATH1). For both experiments three LMPC-derived phloem tissue (LMPC-derived phloem_1-3) and three phloem exudate samples (Phloem exudate_1-3) were analysed. Precise protocols of plant growth, sample harvest, RNA extraction and amplification are provided in Deeken et al., 2008.

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