Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profile of wox5-1 and seu-3 mutants

ABSTRACT: The goal of this dataset was to transcriptionally profile the roots of wox5-1 and seu-3 mutants. To accomplish this, we collected 1mm of tissue from the root tip of each mutant as well as Col-0 as a control. RNA was extracted from root tissue, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE104945 | GEO | 2020/06/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots

Project description:Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem-cell specific transcription factors BRAVO and WOX5 co-localize in the Quiescent Center (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modeling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development.

2021-05-06 | GSE173945 | GEO

Project description:WOX5 maintains columella stem cells in the Arabidopsis root and prevents their differentiation. In order to understand the molecular mode of WOX5 action the genes differentially expressed by WOX5 inducible over-expression were determined by analysis of microarray hybridizations. Seedlings transformed with a dexamethasone inducible WOX5 construct were induced for one or four hours with dexamethasone or a mock solution. Other seedlings were treated one hour with cycloheximide ( a protein synthesis inhibitor to reduce secondary transcriptional effects after WOX5 activation) and either dexamethasone or a mock solution. Root tips were harvested, RNA extracted, and the RNA samples prepared for hybridization to Affymetrix microarrays. Potential target genes of WOX5 were further analyzed by transcriptional markers, qPCR and EMSA (electrophoretic mobility shift assay).

2016-10-16 | E-MTAB-2853 | biostudies-arrayexpress

RNA-seq analysis of callus of Arabidopsis WT and wox5-1 wox7-1

Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.

2021-09-08 | GSE156990 | GEO

Time course of the Arabidopsis root stem cells

Project description:The goal of this dataset was to transcriptionally profile the Arabidopsis root stem cells over developmental time. To accomplish this, we protoplasted roots expressing PET111:GFP every 8 hours from 4 days to 6 days old. We then collected GFP negative cells from the PET111:GFP line using cell sorting, as these cells represent the stem cell population. RNA was extracted from cells, libraries were prepared, and RNA-seq was performed. FPKM values were calulcated using Cufflinks.

2019-10-15 | GSE131988 | GEO

Identification of WOX5 targets in the root of Arabidopsis thaliana

Project description:A chromatin immunoprecipitation-based microarray experiment (ChIP-chip) was performed to identify WOX5 direct target. genes

2025-01-08 | GSE270459 | GEO

Arabidopsis thaliana root tip: ago1-101, scr-3 and Col-0

Project description:Transcription profiling of Arabidopsis thaliana root tip region comparing argonaute1-101 (SALK_035319), scr-3 and wild-type Col-0.

2009-12-31 | GSE16460 | GEO

Identification of WOX5 targets in the root of Arabidopsis thaliana

Project description:Identification of WOX5 targets in the root of Arabidopsis thaliana

| PRJNA1126676 | ENA

Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

Project description:The root cap-specific conversion of the auxin precursor indole-3-butyric acid (IBA) into the main auxin indole-3-acetic acid (IAA) generates a local auxin source which subsequently modulates both the periodicity and intensity of auxin response oscillations in the root tip of Arabidopsis, and consequently fine-tunes the spatiotemporal patterning of lateral roots. To explore downstream components of this signaling process, we investigated the early transcriptional regulations happening in the root tip during IBA-to-IAA conversion in Col-0 and ibr1 ibr3 ibr10 triple mutant after 6 hours of IBA treatment. Arabidopsis thaliana (L). Heynh., Col-0 and ibr1ibr3ibr10 seeds were germinated vertically on solid medium derived from standard Murashige and Skoog (MS) medium. Three days after germination, Col-0 and ibr1ibr3ibr10 seedlings were transferred to a fresh MS medium supplemented with or without 10 ?M indole-3-buytric acid (IBA) for 6 hours. Then, root tip segments (~4mm) were dissected from the primary root and harvested for further RNA extraction. For each treatment, at least 120 individual Col-0 or ibr1ibr3ibr10 mutant root tip segments were sampled and three independent biological replicates were performed. Hormone and DMSO solution were filer-sterilized before being added to the medium.

2015-05-12 | E-GEOD-59426 | biostudies-arrayexpress

Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

2015-05-12 | GSE59426 | GEO

Transcriptome gene expression analysis of root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) from Ceratopteris richardii sporophytes

Project description:To study genes specially expressed in root tip, leaf tip, shoot tip, root (without root tip) and leaf (without leaf tip) of Ceratopteris richardii, we carried out an RNA-seq to analyze gene expression levels from these five tissues.

2019-10-22 | GSE139160 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data