Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana

ABSTRACT: RNA-seq analysis of gene expression levels duing callus formation on CIM using WT and lbd16-2

PROVIDER: PRJNA393995 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5820082_1.fastq.gz	Fastqsanger.gz
	SRR5820082_2.fastq.gz	Fastqsanger.gz
	SRR5820083_1.fastq.gz	Fastqsanger.gz
	SRR5820083_2.fastq.gz	Fastqsanger.gz
	SRR5820084_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Arabidopsis thaliana

Project description:Micro-array analysis of WT and AtISWI in callus formation

| PRJNA245753 | ENA

Gene expression profile during wound-induced callus formation in Arabidopsis thaliana

Project description:Wounding is a primary trigger of organ regeneration but how wound stress reactivates cell proliferation and promotes cellular reprogramming remains elusive. In this study we combined the transcriptome analysis with quantitative hormonal analysis to investigate how wounding induces callus formation in Arabidopsis thaliana. Our time-course RNA-seq analysis revealed that wounding induces dynamic transcriptional changes that can be categorized into five clusters with distinct temporal patterns. Gene ontology analyses uncovered that wounding modifies the expression of hormone biosynthesis and response genes, and quantitative analysis of endogenous plant hormones revealed accumulation of cytokinin prior to callus formation. Mutants defective in cytokinin synthesis and signalling display reduced efficiency in callus formation, indicating that de novo synthesis of cytokinin has major contribution in wound-induced callus formation. We further demonstrate that type-A ARABIDOPSIS RESPONSE REGULATOR (ARR)-mediated cytokinin signalling regulates the expression of CYCLIN D3;1 (CYCD3;1) and mutations in CYCD3;1 and its homologs CYCD3;2-3 cause defects in callus formation. Our transcriptome data, in addition, showed that wounding activates multiple developmental regulators, and we found novel roles of ETHYLENE RESPONSE FACTOR 115 (ERF115) and PLETHORA3 (PLT3), PLT5, PLT7 in wound-induced callus formation. Together, this study provides novel mechanistic insights into how wounding reactivates cell proliferation during callus formation.

2017-10-01 | GSE101422 | GEO

Arabidopsis regeneration from multiple tissues occurs via a root development pathway

Project description:Unlike most animal cells, plant cells can easily regenerate new tissues from a wide variety of organs when properly cultured. The common elements that provide varied plant cells with their remarkable regeneration ability are still largely unknown. Here we describe the initial process of Arabidopsis in vitro regeneration, where a pluripotent cell mass termed callus is induced. We demonstrate that callus resembles the tip of a root meristem, even if it is derived from aerial organs such as petals, which clearly shows that callus formation is not a simple reprogramming process backwards to an undifferentiated state as widely believed. Furthermore, callus formation in roots, cotyledons and petals is blocked in mutant plants incapable of lateral root initiation. It thus appears that the ectopic activation of a lateral root development program is a common mechanism in callus formation from multiple organs. Four sets of biologically independent tissue samples were collect for root, cotyledon and petal explants just after being excised from plants (d0) or after ten days on callus-inducing medium (CIM, d10). Samples derived from the same organ were co-hybridized in the array experiments. Dyes used for labeling the RNA populations derived from the individual samples were switched in the replicate experiments to reduce dye-related artefacts.

2010-01-31 | E-GEOD-19863 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:eif3k/WT transcript levels

| PRJNA143161 | ENA

Micro-array analysis of WT and AtISWI in callus formation

Project description:Plant regeneration could be achieved via formation of a pluripotent cell mass termed callus, nature of which is a group of fast-dividing root primordium cells. However, mechanisms that strictly control the stem cell fate transition in regeneration of callus remain elusive. Here we show that the Arabidopsis ISWI type chromatin remodelers specifically promote the second-step cell fate transition from root founder cells to root primordium cells in the leaf-to-callus transition. Leaf explants cultured in CIM from Col-0 or chr11-1 chr17-1 at time 0 and 8 days after culture (8 DAC) were used for RNA preparation. Microarray was performed using the AffymetrixGeneChip system. Three independent experiments were performed.

2014-05-15 | E-GEOD-57145 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:OBP4 modifies root growth, cell elongation and callus formation

| PRJNA319041 | ENA

Arabidopsis thaliana

Project description:Age-related change of callus formation capability in Arabidopsis hypocotyls

| PRJNA138573 | ENA

RNA-seq analysis of gene expression levels duing callus formation on CIM using WT and lbd16-2

Project description:To study the molecular mechanism of how LBD16 contributes to pluripotency acquisition in callus cells, we performed RNA-seq to analyze its potential downstream genes, using leaf explants from wild-type Col-0 and lbd16-2 before culture (0 d) and at 4 days on CIM. Our study suggests that gain of the root primordium-like identity is the key event for callus to acquire pluripotency, and LBD16 gene is a specific root primordium gene that ensures the callus to be pluripotent.

2017-08-01 | GSE101321 | GEO

Arabidopsis thaliana

Project description:Gene expression profile during wound-induced callus formation in Arabidopsis thaliana

| PRJNA394215 | ENA

Arabidopsis thaliana

Project description:K36me2 levels in WT and sdg7 sdg8

| PRJDB17516 | ENA