Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome of radially growing Arabidopsis wild type and d14 mutant hypocotyls with single cell resolution revealed by nucleus RNA-seq using 10x Chomium and VASA-seq

ABSTRACT: Wood formation is fundamental for the remarkable growth of plant bodies by continuously providing cells for long-distance transport of water and nutrients and for mechanical support. Vessel elements, the water transporting units within woody tissues, are generated from a cylindrical domain of cambium stem cells (CSCs) generating different vascular cell types in a bidirectional manner during the radial (secondary) growth. However, knowledge on the regulation of CSC activity is limited with unclear cell fate trajectories as the most obscure aspect in this context. Here, we provide a transcriptome atlas of CSCs and their derivatives at single cell resolution in Arabidopsis thaliana hypocotyl.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE224928 | GEO | 2023/04/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome profiles and comparison of Arabidopsis thaliana woody (soc1-ful) and WT (Col-0) stems.

Project description:The douple mutant Arabidopsis thaliana soc1 ful, in contrast with WT, produces an interfascicular cambium and a large wood cylinder is the flowering stem. We present the RNAseq data for polyA mRNA of different developmental stages of cambium and wood formation in Arabidopsis thaliana. We sequenced 7 stages; 4 in the woody mutant soc1-6 ful-7 (herbaceous, cambium initiation, wood initiation and leaf) and 3 stages in the WT Col-0 (herbaceous, cambium and leaf). The corresponding stem anatomy is also presented in the manuscript indicating the stage of cambium development and the production of secondary xylem.

2016-05-21 | GSE69167 | GEO

The Populus Homeobox Gene ARBORKNOX2 Regulates Secondary Growth in trees

Project description:Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems. We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems. ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium. Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells. These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation. Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content. Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth. We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.

2009-10-01 | GSE15595 | GEO

Transcription profiling of Arabidopsis short day grown hypocotyls to identify genes involved in secondary cell wall development

Project description:Arabidopsis, when grown under short day conditions (16 hours dark, 8 hours light, 22oC) develop extensive secondary thickened hypocotyls with both a vascular and cork cambium (Chaffey et al, 2002, Phys. Plant., 114:594-600). It has been found that once secondary xylem development is completed within the Arabidopsis hypocotyls, it closely resembles the structure of the wood of angiosperm trees (Chaffey et al, 2002, Phys. Plant., 114:594-600). We can utilise this model Arabidopsis tree to identify genes that are important for secondary cell wall formation in xylem cells and therefore important for wood development. Columbia plants were grown for 3 months under short day conditions and secondary thickened hypocotyls were snap-frozen in liquid nitrogen. RNA was isolated from these hypocotyls and submitted to NASC for probing against the ATH1-121501 full GeneChip. Experiment Overall Design: 2 samples

2008-06-14 | E-GEOD-6153 | biostudies-arrayexpress

Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis

2007-01-22 | GSE6153 | GEO

The regulation of cambial activity in Cunninghamia lanceolata involves extensive transcriptome remodeling

Project description:We sequenced mRNA from dormant, reactivating, and actively growing C. lanceolata vascular cambium using tangential cryosections to generate the first transcriptome dynamics that may serve as a gene expression profile blueprint for cambium development and wood formation in the conifer.

2014-03-31 | GSE37152 | GEO

The regulation of cambial activity in Cunninghamia lanceolata involves extensive transcriptome remodeling

2014-03-31 | E-GEOD-37152 | biostudies-arrayexpress

Identification of transcriptome of nst1-1 nst3-1 plant

Project description:Wood is one of the most important and enormous biomass that is widely used in our life. It is formed by successive addition of secondary xylem that develops continuously from cambium. The transcriptome of nst1 nst3 “double-knockout” lines was examined to know the effect of mutations on wood formation. Keywords: mutant vs wt comparison

2006-10-28 | GSE5187 | GEO

Seasonal variation of primary metabolism in the cambial zone of Eucalyptus grandis

Project description:Wood is formed by the differentiation of cells from the vascular cambium and it is an important source for pulp, paper and bioenergy production. However there is little information about the vascular cambium at the molecular level, particularly in response to seasonality in tropical regions. We used three different molecular approaches: transcripts, proteome and metabolome to characterize the seasonal alterations in the primary metabolism of the eucalyptus cambial zone. Based on 2-DE analysis, 71 proteins were differentially expressed.

2016-07-26 | PXD003504 | Pride

Arabidopsis thaliana 6-day-old dark-grown hypocotyls; Col-0 and shr (LOF)

Project description:Transcriptional profiling of hypocotyl comparing wild type with shr mutant. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SHORT-ROOT on growth and development of Arabidopsis shoot system (hypocotyl) by global transcriptome analysis and to identify the key players in the regulatory pathway.

2021-12-28 | GSE97670 | GEO

Stimulation of cell elongation by tetraploidy in hypocotyls of dark-grown Arabidopsis seedlings

Project description:Transcriptional profiling of diploid and tetraploid Arabidopsis dark-grown hypocotyls. The aim of this study was to identify ploidy-related genes involved in the determination of cell size. This study showed that a group of genes involved in lipid transport/localization/binding were downregulated in a defined region of the tetraploid hypocotyl when compared to the diploid hypocotyl.

2015-07-16 | GSE69349 | 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