Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from poplar apices

ABSTRACT: We studied differences in gene expression between Populus P35S::EBB1 lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by overexpression of the EBB1 gene. By screening activation tagging population, we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth. We fully recapitulated the phenotype by overexpression of the gene into the same genotype under a strong constitutive promoter (P35S::EBB1). We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin. Our data indicates that EBB1 plays an important role in the process of bud-break. Poplar apex was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous native expression of affected genes in P35S::EBB1 lines and control, in order to increase the resolution of expression profiles inducing the developmental changes in P35S::EBB1. To do that, we selected apex tissue from greenhouse healthy plants.

ORGANISM(S): Populus tremula x Populus alba

SUBMITTER: Victor Busov

PROVIDER: E-GEOD-16495 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from amiEBBB1 poplar apices

Project description:We study gene expression Populus amiEBB1 lines affecting dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by expression of artifical micro RNA (ami) targeting EBB1 gene. By screening activation tagging population we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth. We fully recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::EBB1). We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin. Down-regualtion of EBB1 influence negatively bud break. Our data indicates that EBB1 plays a important role in the process of bud-break. Poplar apex was selected for RNA extraction and hybridization on Affymetrix microarrays. We used apices tissue from amiEBB1 grown greenhouse healthy plants.

2014-03-12 | E-GEOD-55813 | biostudies-arrayexpress

Expression data from BIG LEAF

Project description:We study differences in gene expression between Populus P35S::BL (BL-oe) lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by overexpression of BL gene. We identified an activation tagging mutant with increased leaf size and correspondingly name it BIG LEAF (BL). We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes a WD40 putative transcription regulator similar to the Arabidopsis thaliana STERILE APETALA (SAP). We recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::BL, BL-oe). Transgenic up-regulation of the BL gene caused enhanced leaf size, early bud-break, and suppression of secondary growth. BL transcript abundance in wild type plants is in apical tissues, mostly in shoot meristem, leaf primordia and axillary meristem. Our data indicates that BL plays an important role in the process of tree growth. Poplar apex, secondary stem (30th internode), and leaves (at 30 node) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression of affected genes in P35S::BL lines and control wild type (WT-717), in order to increase the resolution of expression profiles inducing the developmental changes in P35S::BL. To do that, we selected apex, stem and leaf tissue from greenhouse healthy plants.

2017-05-11 | E-GEOD-68859 | biostudies-arrayexpress

Expression data from poplar apices

Project description:We studied differences in gene expression between Populus P35S::EBB1 lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by overexpression of the EBB1 gene. By screening activation tagging population, we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth. We fully recapitulated the phenotype by overexpression of the gene into the same genotype under a strong constitutive promoter (P35S::EBB1). We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin. Our data indicates that EBB1 plays an important role in the process of bud-break.

2010-05-28 | GSE16495 | GEO

Expression data from amiEBBB1 poplar apices

2014-03-12 | GSE55813 | GEO

Expression data from BIG LEAF

2017-05-11 | GSE68859 | GEO

Expression data from poplar roots under nitrogen limitation

Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.

2013-07-17 | E-GEOD-43162 | biostudies-arrayexpress

Gene expression profiling of grape-bud response to two alternative dormancy-release stimuli.

Project description:A grape-bud-oriented genomic platform was produced for a large-scale comparative analysis of bud responses to two stimuli of grape-bud dormancy release, hydrogen cyanamide (HC) and heat shock (HS). The results suggested considerable similarity in bud response to the stimuli, both in the repertoire of responding genes and in the temporary nature of the transcriptome reprogramming. Nevertheless, the bud response to HC was slower, more condensed and stronger, as reflected by a higher number of regulated genes and a higher intensity of regulation compared to the response to HS. To facilitate large-scale comparative analysis of early changes in the bud transcriptome by cDNA microarray, HC and HS were applied to canes collected from three vineyards, located in different regions, in three different years. This experimental scheme resulted in two true biological replicates for each treatment, differing in both timing and location, and loop design of technical replicates within time series. Consistent with our previous studies, both application of 5% Dormex (HC) and incubation for 1 h in 50oC water (HS) resulted in increased bud-break rates compared to respective controls. Bud break of HS-treated and HC-treated buds started 10 to 12 days after treatment. Three weeks after treatment, HS-treated buds exhibited 100% bud break while HC-treated buds had reached 80% bud break. The control showed significantly lower levels of bud break during this period. Bud material was collected from control, HC- and HS-treated cuttings at six time points (3, 6, 12, 24, 48 and 96 h) after the treatments and used to prepare total RNA samples.

2010-05-19 | E-GEOD-16173 | biostudies-arrayexpress

Global epigenome analysis reveals the role of histone modifications in the chilling-regulated gene expressions in dormant apple flower buds [RNA-seq]

Project description:Bud dormancy – the repeated phase of rest that punctuates periods of growth in the life cycles of many perennial species. In temperate fruit trees, fulfillment of chilling requirement and subsequent heat requirement enable dormant buds to have uniform blooming in field. However, effects of environmental factors such as chilling underlying dormancy release and bud break has not been fully understood. Histone modification is an important epigenetic regulation system which plays an important role in gene expression in various developmental and adaptive processes. Taking advantage of next-generation sequencing, we generated epigenome and transcriptome profiling at different stages before chilling, after chilling and just before bud break in apple (Malus x domestica). We found H3K27me3 may play dominant role during chilling and the genes involved in lignin and lipid metabolic process showed histone modifications. Interestingly, the higher ratio of genes in chilling-associated network exhibited histone modifications, suggesting crucial epigenetic roles in regulating gene expressions in response to chilling during dormancy. Furthermore, H3K4me3 may play more important role during bud break and the genes related to cell wall modification/organization were strongly modified. Taken together, this study provides important insights into the chromatin-based gene regulation underlying chilling-mediated dormancy release and bud break in apple.

2024-03-31 | GSE171131 | GEO

Global epigenome analysis reveals the role of histone modifications in the chilling-regulated gene expressions in dormant apple flower buds

2024-03-31 | GSE128041 | GEO

Transcription profiling of blackcurrant (Ribes nigrum cv Ben Hope) bud tissue during dormancy and bud-break.

Project description:Transcriptional analysis of staged leaf bud tissue during dormancy and bud-break in blackcurrant using SCRI custom Ribes 4k arrays

2010-05-01 | E-TABM-807 | biostudies-arrayexpress

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