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Single-cell transcriptome of Nicotiana attenuata corolla cells.

ABSTRACT: Single-cell transcriptome of Nicotiana attenuata corolla cells.

PROVIDER: PRJNA796301 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17555533.fastq.gz	Fastqsanger.gz
	SRR17555534.fastq.gz	Fastqsanger.gz
	SRR17555535.fastq.gz	Fastqsanger.gz

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Single-cell transcriptome of Nicotiana attenuata corolla cells.

Project description:High-throughput single-cell RNA sequencing (scRNA-seq) identifies distinct cell populations based on cell-to-cell heterogeneity in gene expression. By examining the distribution of the density of gene expression profiles, we can observe the metabolic features of each cell population. Here, we employ the scRNA-seq technique to reveal the entire biosynthetic pathway of a flower volatile. The corolla of the wild tobacco Nicotiana attenuata emits a bouquet of scents that are composed mainly of benzylacetone (BA). Protoplasts from the N. attenuata corolla limbs and throat cups were isolated at three different time points, and the transcript levels of >16,000 genes were analyzed in 3,756 single cells. We performed unsupervised clustering analysis to determine which cell clusters were involved in BA biosynthesis. The biosynthetic pathway of BA was uncovered by analyzing gene co-expression in scRNA-seq datasets and by silencing candidate genes in the corolla. In conclusion, the high-resolution spatiotemporal atlas of gene expression provided by scRNA-seq reveals the molecular features underlying cell-type-specific metabolism in a plant.

2022-02-08 | GSE193464 | GEO

Nicotiana attenuata

Project description:Nicotiana attenuata overview

| PRJNA135343 | ENA

SuperSAGE analysis of the Nicotiana attenuata transcriptome after wounding

Project description:Fatty acid-amino acid conjugates (FACs) in the oral secretion (OS) of the Manduca sexta larvae are necessary and sufficient to elicit the herbivory-specific responses in Nicotiana attenuata, an annual wild tobacco species. We used SuperSAGE combined with 454 sequencing to quantify the early transcriptional changes elicited by the FAC N-linolenoyl-glutamic acid (18:3-Glu) in N. attenuata. The second fully expanded leaf of rosette stage plants were wounded by rolling a fabric pattern wheel three times on each side of the midvein and the wounds were immediately supplied with either 20 uL of 0.02% (v/v) Tween-20/water (solvent control) or 10 uL of synthetic N-linolenoyl-glutamic acid (18:3-Glu; 0.03 nmol/ÂµL in 0.02% (v/v) Tween-20/water). Tissue was collected after 30 min of the treatments and frozen in liquid nitrogen. Total RNA was extracted by the phenol/chloroform-LiCl method and poly(A)+-RNA was purified from total RNA. Subsequent steps for the construction of the SuperSAGE libraries and 454 sequencing were performed as previously described using double NlaIII digestions (Molina et al., 2008, BMC Genomics, 9:553). Two SuperSAGE libraries were generated after wounding and FAC elicitation of Nicotiana attenuata leaves. Leaves were harvested after 30 min of the treatments, total RNA extracted, polyA+ mRNA isolated and used for cDNA synthesis and SuperSAGE analysis as described my Matsumura et al (2003).

2010-10-05 | E-GEOD-18595 | biostudies-arrayexpress

Nicotiana attenuata

Project description:Nicotiana attenuata Raw sequence reads

| PRJNA942061 | ENA

Characterization of Nicotiana attenuata plants with reduced expression of HSPRO (ir-hspro plants).

Project description:Identification of transcripts that change expression in roots of Nicotiana attenuata plants with reduced expression of HSPRO and in association with Piriformospora indica. Gene expression in roots of Nicotiana attenuata wild type and ir-hspro seedlings was measured at 14 days after inoculation with Piriformospora indica. Three independent experiments were performed with wild type plants and three independent experiments were performed with ir-hspro plants.

2012-11-06 | E-GEOD-35086 | biostudies-arrayexpress

JAZi-mediated jasmonate signaling is invoved in floral defense in Nicotiana attenuata

Project description:Identification of transcripts that change expression in Nicotiana attenuata plants with reduced expression of JAZi in flowers

2017-07-12 | GSE101143 | GEO

TOC1 silencing in roots only changes transcriptional responses to drought in Nicotiana attenuata

Project description:Identification of transcripts that change expression in TOC1-silenced Nicotiana attenuata plants leaves and roots under drought

2019-01-08 | GSE124736 | GEO

Nicotiana attenuata

Project description:Nicotiana attenuata Transcriptome or Gene expression

| PRJNA490041 | ENA

Nicotiana attenuata

Project description:Nicotiana attenuata AZ-2019 MAGIC eQTL

| PRJNA911202 | ENA

NaMYC2 transcription factor regulates a subset of plant defense responses in Nicotiana attenuata

Project description:Identification of significantly altered transcripts in Nicotiana attenuata plants with reduced MYC2 expression after induction with oral secretions of Manduca sexta larvae. Gene expression in leaves of Nicotiana attenuata EV and MYC2_VIGS plants was measured at 1 hour after induction with oral secretions of Manduca sexta larvae. Three independent experiments were performed with EV plants and three independent experiments were performed with MYC2_VIGS plants. A total of 47 genes were identified as differentially regulated in MYC2_VIGS plants compared to EV plants.

2013-05-17 | E-GEOD-45608 | biostudies-arrayexpress

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