Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time-lapse RNA-seq analysis to study the gene networks in cell fate transition in de novo root regeneration from detached Arabidospis leaves

ABSTRACT: Time-lapse RNA-seq analysis to study the gene networks in cell fate transition in de novo root regeneration from detached Arabidospis leaves

PROVIDER: PRJNA613690 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11359530_1.fastq.gz	Fastqsanger.gz
	SRR11359530_2.fastq.gz	Fastqsanger.gz
	SRR11359531_1.fastq.gz	Fastqsanger.gz
	SRR11359531_2.fastq.gz	Fastqsanger.gz
	SRR11359532_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 62

Similar Datasets

Time-lapse RNA-seq analysis to study the gene networks in cell fate transition in de novo root regeneration from detached Arabidospis leaves

Project description:Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed time-lapse RNA-seq within 5 d revealed activation of gene networks in cell fate transition.

2022-02-10 | GSE147296 | GEO

Time-lapse RNA-seq analysis to study transcriptional regulation by early signals in De Novo Root Regeneration in Arabidopsis

Project description:Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed time-lapse RNA-seq within 12 h to reveal transcriptional changes in response to early signals in DNRR.

2022-02-10 | GSE147301 | GEO

Transcriptional landscapes of de novo root regeneration from detached Arabidopsis leaves revealed by time-lapse and single-cell RNA sequencing analyses.

Project description:Detached Arabidopsis thaliana leaves can regenerate adventitious roots, providing a platform for studying de novo root regeneration (DNRR). However, the comprehensive transcriptional framework of DNRR remains elusive. Here, we provide a high-resolution landscape of transcriptome reprogramming from wound response to root organogenesis in DNRR and show key factors involved in DNRR. Time-lapse RNA sequencing (RNA-seq) of the entire leaf within 12 h of leaf detachment revealed rapid activation of jasmonate, ethylene, and reactive oxygen species (ROS) pathways in response to wounding. Genetic analyses confirmed that ethylene and ROS may serve as wound signals to promote DNRR. Next, time-lapse RNA-seq within 5 d of leaf detachment revealed the activation of genes involved in organogenesis, wound-induced regeneration, and resource allocation in the wounded region of detached leaves during adventitious rooting. Genetic studies showed that BLADE-ON-PETIOLE1/2, which control aboveground organs, PLETHORA3/5/7, which control root organogenesis, and ETHYLENE RESPONSE FACTOR115, which controls wound-induced regeneration, are involved in DNRR. Furthermore, single-cell RNA-seq data revealed gene expression patterns in the wounded region of detached leaves during adventitious rooting. Overall, our study not only provides transcriptome tools but also reveals key factors involved in DNRR from detached Arabidopsis leaves.

| S-EPMC9284295 | biostudies-literature

effect of sucrose feeding to detached leaves

2008-01-05 | GSE4022 | GEO

Methanol is an endogenous elicitor molecule upon senescence of detached rice leaves

Project description:During senescence of detached rice leaves, tryptophan (Trp) and Trp-derived secondary metabolites such as serotonin and 4-coumaroylserotonin accumulated in concert with methanol (MeOH) production. This senescence-induced MeOH induction was closely associated with levels of pectin methylesterase (PME)1 mRNA and PME enzyme activity. Exogenous challenge of detached rice leaves with 1% MeOH accelerated Trp and serotonin biosynthesis with induction of the corresponding genes. No other solvents including ethanol resulted in a Trp-inducing effect. This MeOH-induced Trp synthesis was positively regulated by abscisic acid but negatively regulated by cytokinin, suggesting hormonal involvement on the action of MeOH. Endogenous overproduction or suppression of MeOH either by PME1 overexpression or RNAi gene silencing revealed that PME1 overexpressing lines produced twofold higher Trp levels with elevated Trp biosynthetic gene expression, whereas RNAi lines showed twofold reduction in Trp level in healthy control rice leaves, suggesting that MeOH acts as an endogenous elicitor to enhance Trp biosynthesis. Among many transcription factors induced following MeOH treatment, the WRKY family showed significant induction patterns of which WRKY14 appeared to play a key regulatory role in MeOH-induced Trp and Trp-derived secondary metabolite biosynthesis. Total RNAs were extracted from the detached rice leaves with 1% MeOH or distilled water for 1 d, and gene expression was compared between the two groups with two replicates. DW, detached leaves in distilled water for 1 day; MeOH (2-replications), methanol treated detached leaves at the same time point as control. 2 sets of separately normalized data; DW-MeOH(1) and MeOH(2).

2011-01-03 | E-GEOD-26387 | biostudies-arrayexpress

Single-Cell RNA-seq analysis of cell lineages in De Novo Root Regeneration

Project description:Detached Arabidopsis leaves can regenerate adventitious roots, providing a platform to study de novo root regeneration (DNRR). We performed single-cell RNA-seq analysis and revealed that regeneration primarily originated from vascular stem-cell organizer within procambium, followed by step-by-step changes of transcriptome in cell fate transition, including gradually erasing the vascular stem-cell organizer identity and recruiting the root development program.

2022-02-10 | GSE147289 | GEO

Transcription profiling of Arabidopsis response to sucrose feeding to detached leaves

Project description:The effect of sucrose feeding on gene expression in Arabidopsis thaliana leaves was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis. Experiment Overall Design: The effect of sucrose feeding on gene expression was investigated using affymetrix ATH1 microarrays. For this, petioles of detached leaves were put in a solution containing either sucrose or sorbitol (control). Sugars were taken up into the leaf via the respiration stream for 13 hours. After that, leaves were frozen in liquid nitrogen and RNA was extracted for analysis.

2008-06-12 | E-GEOD-4022 | biostudies-arrayexpress

Methanol is an endogenous elicitor molecule upon senescence of detached rice leaves

2011-01-03 | GSE26387 | GEO

Functional Analysis of CLE26 in Controlling De Novo Root Regeneration from Detached Arabidopsis Leaves.

Project description:De novo root regeneration is the process by which adventitious roots form around the wound site from wounded or detached plant organs. The de novo root regeneration process has been widely exploited in cutting technology used for vegetative propagation. Here, we employed detached leaf explants from Arabidopsis thaliana to form adventitious roots for studying the process of de novo root regeneration. GUS staining showed that the expression of CLAVATA3/EMBRYO SURROUNDING REGION-RELATED26(CLE26) was gradually increased surrounding the wound site of leaf explants during adventitious root formation. Semi-thin sections further showed that the expression pattern of CLE26 was closely linked to the formation of adventitious roots. Next, genetic analyses confirmed that the CLE26 gene was involved in de novo root regeneration. Furthermore, RNA sequencing (RNA-seq) of the leaf explants revealed that stress-related genes might be involved in CLE26-mediated adventitious root formation. Specifically, genes associated with the hydrogen peroxide catabolic process and oxidative stress response were predominantly upregulated in the cle26 mutant. In contrast, genes involved in the response to salicylic acid were largely downregulated in the cle26 mutant. Overall, our study indicates that the mutation in CLE26 might upregulate the expression of genes involved in reactive oxygen species metabolism or suppress the expression of genes associated with salicylic acid synthesis, thus promoting the formation of adventitious roots. These findings suggest that CLE26 is a potential candidate for the genetic improvement of adventitious rooting in cuttings.

| S-EPMC11642536 | biostudies-literature

Time-lapse RNA-seq analysis to study transcriptional regulation by early signals in De Novo Root Regeneration in Arabidopsis

Project description:Time-lapse RNA-seq analysis to study transcriptional regulation by early signals in De Novo Root Regeneration in Arabidopsis

| PRJNA613702 | ENA