Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

ABSTRACT: To analyze the molecular mechanism behind the relationship between Arabidopsis leaf maturation and de novo root regeneration, we carried out an RNA-seq analysis using detached first-pair rosette leaves before culturing (time 0) and 1 d after culturing (DAC) from 9-, 12- and 15-d-old Col-0 seedlings. We first analyzed gene expression levels in the leaves before detachment (at time 0) from the three developmental states. Changes in gene expression could be grouped into six clusters. Many genes were upregulated or downregulated during leaf maturation. Next, we analyzed gene expression levels in the leaf explants from 9- and 15-d-old seedlings at 1 DAC compared with gene expression levels at time 0. By comparing up- or downregulated genes (1 DAC vs time 0) between leaves from 9- and 15-d-old seedlings, we found that many of the genes were particularly up- or downregulated only in immature leaves or only in mature leaves after 1 d of culturing.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE108253 | GEO | 2018/12/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome-wide analysis of wounded region gene expression using detached first-pair rosette leaves before culture (time 0) and 2 day after culture (DAC) from 12-day-old Col-0 seedlings

Project description:To reveal the molecular mechanism during de novo root regeneration from Arabidopsis leaf explants cultured on B5 medium without exogenous hormones, we carried out an RNA-seq experiment using detached leaf explants with partial petiole before culture (i.e. time 0) and 2 d after culturing (DAC) from12-d-old Col-0 seedlings. Gene expression of the wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was analyzed.

2019-10-22 | GSE139165 | GEO

Expression data from aerial parts of 14-day-old wild-type and GFP-TIE1-15 Arabidopsis seedlings

Project description:TIE1 regulates leaf development by repressing leaf differentiation because the semi-dominant mutant tie1-D by activation tagging displays small and hyponastic leaves and the differentiation of leaf epidermal cells is delayed in the tie1-D mutant, whereas disruption of TIE1 causes epinastic leaves with early differentiated epidermal cells. We used microarrays to investigate the molecular base underpinning the phenotypes of TIE1-overexpressing plants. Aerial parts of 14-day-old seedlings from wild-type and GFP-TIE1-15 were collected for RNA extraction and hybridization on Affymetrix microarrays.

2012-05-26 | E-GEOD-38282 | biostudies-arrayexpress

Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

Project description:Transcriptome-wide analysis of gene expression using detached first-pair rosette leaves before culture (time 0) and 1 day after culture (DAC) from 9-day-old, 12-day-old and 15-day-old Col-0 seedlings

| PRJNA422982 | ENA

Expression data from aerial parts of 14-day-old wild-type and GFP-TIE1-15 Arabidopsis seedlings

2012-05-27 | GSE38282 | GEO

Transcriptome-wide analysis of wounded region gene expression using detached first-pair rosette leaves before culture (time 0) and 2 day after culture (DAC) from 12-day-old Col-0 seedlings

Project description:Transcriptome-wide analysis of wounded region gene expression using detached first-pair rosette leaves before culture (time 0) and 2 day after culture (DAC) from 12-day-old Col-0 seedlings

| PRJNA578672 | ENA

Divergent N-deficiency-dependent senescence initiation and transcriptome response in developmentally old and young Brassica napus leaves

Project description:To identify oilseed rape genes with a potential role in N-remobilization during leaf senescence of developmentally old leaves in the lower canopy and young leaves in the upper canopy, transcriptomes of leaf number 4 and leaf number 8 of B. napus (cultivar Mozart) were analysed at different harvest time points under mild N deficiency and optimal N fertilization.

2018-02-01 | GSE97653 | GEO

Microarray analysis of gene expression of the Arabidopsis leaf and callus

Project description:Callus formation is usually a necessary step in regenerating a new plant from detached plant tissues, and the nature of the callus is similar to that of the root meristem. In this study, we intended to address the molecular basis that directs different plant tissues to form the root-meristem-like callus. We found that leaves, but not roots, of the Polycomb group (PcG) double mutant curly leaf-50 swinger-1 lost the ability to form a callus. Using ChIP-chip analysis, we identified genes that are changed markedly in the histone H3 lysine 27 trimethylation (H3K27me3) levels during callus formation from leaf explants. Among these genes, a number of leaf-regulatory genes were repressed through PcG-mediated H3K27me3. Conversely, certain auxin pathway genes and many root-regulatory genes were derepressed through H3K27 demethylation. Our data indicate that genome-wide H3K27me3 reprogramming, through the PcG-mediated H3K27me3 and the H3K27 demethylation pathways, is critical in directing cell fate transition. This submission represents the gene expression component of the study Leaves from 20-day-old seedlings of wild-type Col-0 and 20-DAC calli were used for RNA preparation.

2012-04-06 | E-GEOD-36479 | biostudies-arrayexpress

RNA-seq of etiolated 9 day old maize seedling second leaves after exposure to either blue, red or no light conditions for three hours

Project description:Characterisation of the differences in transcript abundance between maize leaves that have been exposed to blue, red, or no light: B73 maize seeds were planted and grown in the dark for 9 days. Etiolated second leaves were clamped 5 cm from the leaf tip by a Licor 6800 device equipped with a multi-phase flash fluorometer head, which administered 100 µmol m-2s-1 of either 100% red or 100% blue light. The Licor was configured with flow rate 500 µmol s⁻¹, 400 µmol mol⁻¹ CO2, leaf temperature 28°C and 60% humidity. Fluorescence and gas exchange were measured every 15 minutes for 3 hours. Leaf samples were collected between 12.30am-2pm each day.

2019-06-10 | E-MTAB-7200 | biostudies-arrayexpress

RNA profiling of Col-0 and vil1-1 1-day-old seedlings in Arabidopsis

Project description:1-day-old seedlings of Col-0 and vil1-1 were performed RNA-Seq to identify differentially expressed genes caused by VIL1 mutation in Arabidopsis

2022-11-23 | GSE180587 | GEO

Global gene expression in WT and antisense-acetyl-CoA (ACLA) mutant under short day conditions

Project description:Transcriptome analysis of RNA samples from WT and antisense-acetyl-CoA (ACLA) mutant. The antisense-ACLA mutant and WT plants were arranged according to a Randomized Complete Block Design. The plants were planted in rows with seven rows in each flat; two plants of the same genotype/pot. Plants were grown under a SD photoperiod (8 h light/16 h dark) in a growth chamber as described. Eight randomly selected rows were harvested for each time point from different flats. Plant material was harvested at 11 time points in the diurnal cycle (0, 0.5,1, 4, 6, 8,12 h in the dark condition, and 0, 0.5, 1, 4 h in the light condition; Time 0 is the beginning of the light/dark period); harvesting was conducted under a green safety light. Each sample consisted of rosette leaves (leaves 5 to 8, staged following Bowmann (1994); photosynthetically active (Stessman et al., 2002)) from sixteen six-week-old plants. Leaf samples were frozen in liquid N2 immediately after harvest and stored at -80‚°C for RNA extraction. The experiment was done twice and independent randomizations for plant growth and harvest were used for the two replicates.

2024-11-22 | GSE254150 | 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