Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inferring gene regulatory networks that control maintenance and identity of the Arabidopsis root stem cells

ABSTRACT: We isolated QC and xylem cells by sorting GFP+ cells marked with pWOX5::GFP and pTMO5::GFP respectively. We obtained cell-type specific transcriptional profiles of QC and xylem cells.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE76710 | GEO | 2017/09/18

SECONDARY ACCESSION(S): PRJNA308438

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Inferring Gene Regulatory Networks that control maintenance and identity of the Arabidopsis Root Stem Cells

Project description:We isolated QC cells and obtained their cell-type specific transcriptional profiles in a WT and in a pan mutant background by sorting GFP+ cells marked with pWOX5::GFP.

2017-09-18 | GSE97792 | GEO

From gene networks to network motif dynamics: how the presense of positive feed-back and -forward loops between PERIANTHIA, WUSCHEL-RELATED HOMEOBOX5 and GRF-INTERACTING FACTOR 1 modulates gene expression and function in the Arabidopsis roots.

Project description:We isolated QC and CEI cells and obtained their cell-type specific transcriptional profiles in a WT and in a wox5 mutant background by sorting GFP+ cells marked with pWOX5::GFP and pCYCD6::GFP.

2019-08-01 | GSE118102 | GEO

Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [w5C6]

Project description:We performed a transcriptome analysis on FACS-sorted GFP positive cells from pCYCD6;1-GFP, wox5xpCYCD6;1-GFP, and pWOX5-GFP, and the GFP negative cells from pWOX5-GFP to obtain CEI specific transcriptional profiles in a WT and in a wox5 mutant background.

2020-12-31 | GSE155463 | GEO

Transcriptional profiling of the Arabidopsis root quiescent center

Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the AGL42 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5. Three replicates of FACS-sorted GFP-positive cells from WOX5:GFP roots.

2014-12-17 | E-GEOD-64253 | biostudies-arrayexpress

A Mobile miR160-Triggered Transcriptional Axis Controls Root Stem Cell Niche Maintenance and Regeneration in Arabidopsis

Project description:In multicellular organisms, communication between cells is vital for their fate determination. In plants, the quiescent center (QC) signals to adjacent stem cells to maintain them undifferentiated. However, how surrounding stem cells instruct the QC remains poorly understood. Here we show that in the Arabidopsis root, microRNA160 (miR160) moves from vascular stem cells to the QC, where it degrades the mRNAs of two auxin response factors, ARF10 and ARF17. This degradation relieves BRAVO from direct transcriptional repression, maintaining QC quiescence. We further identify that blocking miR160 movement due to DNA damage-induced vascular stem cell death and restricted symplastic transport reduces BRAVO and WOX5 expression, leading to QC division to replenish damaged stem cells during root regeneration. Together, our results demonstrate that a transcriptional axis initiated by mobile miR160 regulates the QC and stem cell behavior, advancing our understanding of the communication between stem cells and their surrounding cellular environment.

2024-09-27 | GSE255979 | GEO

Transcriptional profiling of the Arabidopsis root quiescent center

Project description:The Arabidopsis quiescent center (QC) is a small group of cells with low mitotic activity located at the center of the root stem cell niche. Its transcriptional profile was previously analyzed using two repeats of cells FACS isolated using the WOX5 marker. To get more power in analyzing QC transcriptional profile, we generated three additional samples of the QC, using the QC-specific marker WOX5.

2014-12-17 | GSE64253 | GEO

Cell type-specific auxin responses in the Arabidopsis thaliana root

Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.

2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress

Vascular specific H3K27me3 and H3K4me3 profile in the Arabidopsis root

Project description:We isolated Vascular specific root protoplast using the pWOL:GFP marker line (Birnbaum et al., 2003) and Fluorescence Activated Cell Sorting (FACS). FACS-treated root protoplast from wild type plants (Col0) were used as control. The GFP positive protoplast from the pWOL:GFP line and WT protoplast were used for a ChIP-seq experiment using H3K27me3 and H3K4me3 antibodies.

2016-09-06 | GSE86429 | GEO

A regulatory circuit for maintenance and regeneration of root patterning

Project description:We directed expression of BLUEJAY, JACKDAW and SCARECROW through the UAS promoter in the J0571 line and performed cell sorting followed by microarray experiments to identify differentially expressed genes.

2023-07-28 | GSE155439 | 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

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