Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-GEOD-9728

ABSTRACT: Transcription profiling by array of Arabidopsis mutant for csn after growth in light and dark conditions

OTHER RELATED OMICS DATASETS IN: PRJNA103645

PROVIDER: E-GEOD-9728 | ExpressionAtlas | 2014-07-10

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-GEOD-9728-analysis-methods.tsv	Tabular
	E-GEOD-9728-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-9728-configuration.xml	Xml
	E-GEOD-9728-percentile-ranks.tsv	Tabular
	E-GEOD-9728.condensed-sdrf.tsv	Tabular

Items per page:

1 - 5 of 148

Similar Datasets

COP9 signalosome (csn) mutant analysis

2008-04-24 | GSE9728 | GEO

Transcription profiling of Arabidopsis csn3-1, csn4-1 and csn5 (csn5a-2 csn5b) COP9 signalosome (csn) mutant analysis

Project description:Transcript profiling analysis of csn3-1, csn4-1 and csn5 (csn5a-2 csn5b) light grown and dark grown mutant seedlings compared to light grown and dark grown wild type using Arabidopsis ATH1 GeneChip array Experiment Overall Design: We compare eight samples of 7 day-old light grown or dark grown csn3-1, csn4-1, and csn5 (csn5a-2 csn5b) mutant seedlings and light grown and dark grown wild type seedlings (3 independent biological replicates each).

2008-06-16 | E-GEOD-9728 | biostudies-arrayexpress

Expression data in Arabidopsis hda6 mutant axe1-5 and its parental line DR5 under cold and control conditions.

Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used. Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in MS agar plates for 2 weeks (16 hours light / 8 hours dark). For cold treated sample, the plants were subjected for cold treatment at 2?C for 3 days (12 hours light / 12 hours dark). Then total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

2011-01-27 | E-GEOD-26873 | biostudies-arrayexpress

Genome-wide analysis of toc1-2 transcriptional networks

Project description:To gain insights into the mechanisms of TOC1 function in the Arabidopsis circadian clock we performed transcriptional profiling of Wild-Type (WT) and and TOC1 mutant plants (toc1-2) under constant light conditions for two days. Comparisons of WT and toc1-2. Two biological replicates each per array. Two Arabidopsis Oligonucleotide Microarrays (two-color Cy3 and Cy5). synchronized under 12-hour light:12-hour dark (LD) cycles for 10 days followed by two days under constant light conditions. Samples were collected at circadian time 16 (CT16).

2010-05-05 | E-GEOD-18001 | biostudies-arrayexpress

SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.

2017-08-10 | GSE85883 | GEO

Expression data in Arabidopsis Col-0 with cold acclimation (CA) treatment and subsequent cold deacclimation (DA) treatment.

Project description:To understand mRNA expression pattern during cold acclimation and deacclimation, transcriptional profiling of cold acclimation and deacclimation-treated plants were analyzed using Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F. Arabidopsis Col-0 were grown on MS plate for 2 weeks (16 hours light / 8 hours dark). Two week-old Arabidopsis samples (NA, non acclimation) were treated with cold (2 M-BM-:C) for 7 days (CA7d) under 12h/12h light/dark conditions. Deacclimation-treated samples (DA6h, DA12h, DA24h) were grown at normal growth temperature under long day conditions after cold treatment for 7 days. Then total RNA was prepared from the whole seedling and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.

2014-10-02 | E-GEOD-49796 | biostudies-arrayexpress

CSN4-1 mutant analysis

Project description:Transcript profiling analysis of csn4-1 light grown mutant seedlings compared to wild type using Arabidopsis ATH1 GeneChip array Keywords: 7 day old light grown seedlings, wild type and mutant

2008-03-25 | GSE3865 | GEO

Gene expression in luh mutant seeds in the dark: wild type (Col-0) vs. luh mutant

Project description:Transcriptional profiling of Arabidopsis far-red light pulse treated seeds comparing luh mutant with wild type (Col-0). Seeds were imbibed within 1 hr under white light and treated far-red light pulse for 5 min followed by 12 hr dark incubation. Goal was to determine the effects of LUH as transcriptional co-regulator during seed germination process.

2015-09-27 | GSE70406 | GEO

Arabidopsis dark-induced senescence: wild type (Col-0) vs. pif quadruple (pif1pif3pif4pif5) mutant

Project description:Transcriptional profiling of Arabidopsis dark-induced senescence comparing wild type (Col-0) with pif quadruple (pif1/3/4/5) mutant. After synchronized germination, the plants were grown under continuous white light for 7 days and transferred to darkness for 2 days to induce senescence. Goal was to determine the effect of PIFs on transcriptomic regulation during dark-induced senescence.

2014-08-04 | GSE52646 | GEO

Coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/ER stress and innate immunity pathways by inducible artificial microRNA silencing of the SNF4 activator subunit of Arabidopsis SnRK1

Project description:Arabidopsis SnRK1 is structurally and functionally related to the yeast Snf1 and mammalian AMP-activated kinases, which are activated in response to carbon/glucose limitation and stress conditions causing an imbalance of energy homeostasis increasing the AMP/ATP ratio. Mutations of the SNF4 activating subunit of trimeric Arabidopsis SnRK1 complexes are not transmitted through the male meiosis. Silencing of SNF4 by a β-estradiol-inducible artificial microRNA (amiR-SNF4) constructs was used to examine how inhibition of SnRK1 affects transcriptional regulation of different cellular pathways in dark and light grown seedlings. This study shows that amiR-SNF4 silencing of SnRK1 leads to coordinate transcriptional activation of salicylic acid and trehalose synthesis, oxidative/endoplasmic reticulum stress and pathogen defense responses by inducing simultaneous changes in numerous other essential hormonal and metabolic pathways in Arabidopsis. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and β-estradiol-induced amiR-SNF4 mutant seedlings 5 days after germination in the dark or light.

2016-05-01 | GSE72674 | 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