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

Dark grown Arabidopsis seedlings treated with cytokinin

ABSTRACT: Arabidopsis seed lings were grown in dark for 10 days on MS media and treated with DMSO (control) or 1 µM of BA for either 45 or 120 minutes to look for changes in genes profiles

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Apurva Bhargava

PROVIDER: E-MTAB-1597 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis.

Bhargava Apurva A Clabaugh Ivory I To Jenn P JP Maxwell Bridey B BB Chiang Yi-Hsuan YH Schaller G Eric GE Loraine Ann A Kieber Joseph J JJ

Plant physiology 20130322 1

Cytokinins are N(6)-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin as well as to query the response of genes not represented on microarrays. To this end, we performed a meta-analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Microarray meta-analysis using 13 microarray ...[more]

PMID: 23524861

Similar Datasets

Arabidopsis seedlings and cytokinin

Project description:Aim of this experiment was to look at the gene expression differences in the benzyladenine-treated and untreated Arabidopsis seedlings grown in light

2013-03-27 | E-MTAB-1596 | biostudies-arrayexpress

Arabidopsis seedling treated with BA and Zeatin

Project description:Aim was to look at the gene profile changes in 10 days old Arabidopsis seedlings grown in light and treated with either Zeatin or BA and compared to non-treatment

2013-03-28 | E-MTAB-1601 | biostudies-arrayexpress

Identification of genes cooperatively regulated by cytokinin and HD-ZIP III transcription factors

Project description:In Arabidopsis thaliana, cytokinin responsive B-type ARR transcription factors and HD-ZIP III transcription factors such as REVOLUTA (REV), act cooperatively as master regulators of shoot regeneration. To identify the downstream targets of ARR-HD-ZIP III transcriptional complex, we used an inducible line of REV, 35S::FLAG-GR-rREV, in which FLAG-tagged miR165/6-non-targetable form of REV (rREV)-GR fusion protein was expressed from 35S promoter. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. We treated 35S::FLAG-GR-rREV seedlings with 6-benzylaminopurine (6-BA, a cytokinin), dexamethasone (DEX), or 6-BA+DEX for 2 hours. Total RNAs were extracted and subjected to Agilent Arabidopsis Gene Expression Microarray analyses. The differentially expressed genes (>1.5-fold, p<0.05) were identified. 10-day-old 35S::FLAG-GR-rREV plants were treated with 6-benzylaminopurine (6-BA), dexamethasone (DEX), or 6-BA+DEX for 2 hours. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. Total RNA was extracted with RNeasy Mini Kit and hybridized to Agilent Arabidopsis Gene Expression Microarray. Differentially expressed genes were defined by a 1.5-fold expression difference with a P value<0.05. Biological replicates were performed.

2014-01-29 | E-GEOD-54469 | biostudies-arrayexpress

Transcription profiling by array of wild type and arr1,10,12 mutant Arabidopsis seedlings treated with the cytokinin benzyladenine

Project description:Effect of the cytokinin BA on wt and arr1,10,12 mutant seedlings

2008-06-01 | E-MEXP-1573 | biostudies-arrayexpress

Transcription profiling time series of Arabidopsis seedlings treated with the cytokinin benzyladenine or DMSO

Project description:10 day old seedlings were treated with 5uM of the cytokinin Benzyladenine(BA)or DMSO at 15min, 45min, 120min, 480min and 1440min

2006-08-24 | E-MEXP-749 | biostudies-arrayexpress

Transcription profiling of Arabidopsis plants (tup3 mutant and Col-0gl) in cotyledon stage after treatmeant with cytokinin or auxin for different times

Project description:RNA was extracted from whole Arabidopsis plants(tup3 mutant and Col-0gl)in cotyledon stage under treatmeant (different times: 0 min, 15 min, 120 min) with cytokinin (1 µM BA) and/or auxin (1µM NAA).

2006-10-31 | E-CAGE-49 | biostudies-arrayexpress

Expression data from arabidopsis root in response to boron toxicity

Project description:Boron is an essential micronutrient for plants and is taken up in the form of boric acid (BA). Despite this, a high BA concentration is toxic for the plants, inhibiting root growth and is thus a significant problem in semi-arid areas in the world. In this work, we report the molecular basis for the inhibition of root growth caused by boron. We used microarrays to detail the global gene expression underlying boron toxicity in roots. 5-day-old arabidopsis plants were transferred to medium with high boron concentration (½ MS medium supplemented with 5mM BA) and control conditions (½ MS medium). We determined that 5 mM BA is the minimum concentration that produces the maximum effect, stunting root growth by ~50% after 5 days as compared with control conditions. We analyzed the transcript profiles in roots by microarray analysis (Affymetrix ATH1 Genome Array). We compared the transcripts obtained at 12 hrs of BA treatment.

2011-11-01 | E-GEOD-32659 | biostudies-arrayexpress

Transcriptional analysis of exogenously supplied and transgenic of senescence-induced cytokinin for broccoli postharvest yellowing improvement

Project description:Both exogenously supplied and transgenic induced cytokinin production can effectively delay senescence of broccoli florets during postharvest storage. However, a substantial comparison between the mechanisms of these two treatments on delaying broccoli florets senescence was absent. Here, we conduct microarray analysis on broccoli florets of N6-benzylaminopurine treated and ipt-transgenic broccoli that harbor a senescence-associated-gene promoter triggering isopentenyltransferase gene expression during postharvest storage. Analysis used RNA of Green King inbred line 104 as control sample for comparison to the experimental samples of ipt-transgenic line 102, 103 and parental line Green King as well as 10 ppm BA treated Green King at harvest and after postharvest storage at 25 centigrade in the dark for 4 days.

2013-05-01 | E-GEOD-42609 | biostudies-arrayexpress

Identification of universally applicable and species-specific marker peptides for Bacillus anthracis

Project description:Anthrax is a zoonotic infection caused by the bacterium Bacillus anthracis (BA), a gram-positive, aerobic, spore-forming bacterium that can be misused as a biowarfare agent. The major patho-genicity factors of BA are encoded by genes located on two extrachromosomal plasmids, which are often targeted for specific identification of this pathogen. However, more recent findings show that these plasmids are not a unique feature of BA but can also occur in other Bacillus species. Furthermore, BA is a member of the Bacillus cereus group, a subgroup of closely related Bacilli. Due to the high genetic similarity within this group, it is a challenge to distinguish BA from other members of this group. In this study, we investigated if it is possible to identify species-specific and universally applicable marker peptides for BA. For this purpose, we applied a high-resolution mass spectrometry-based approach for 42 BA isolates. Together with the genomic sequencing data and by developing a bioinformatics data evaluation pipeline, which uses a database containing most of the publicly available protein sequences worldwide (UniParc), we were able to identify eleven universal marker peptides unique to BA, which are located on the chromosome and there-fore might overcome known problems like observable loss of plasmids in environmental species, plasmid loss during cultivation in the lab and that the virulence plasmids are not necessarily a unique feature of BA. The identified chromosomally encoded markers in this study could extend the small panel of already existing chromosomal targets and together with targets for the viru-lence plasmids may pave the way to an even more reliable identification of BA using genomics- as well as proteomics-based techniques.

2023-01-05 | PXD036243 | Pride

Transcription profiling of Arabidopsis wild type, 35S-ARR7, arr7 and 35S-ARR15 treated with cytokinin, auxin or both

Project description:Above ground tissue of 10 day old Arabidopsis seedlings of Col wild-type, 35S-ARR7, arr7, 35S-ARR15 was treated with Cytokinin (benzyladenine), Auxin (indole-3-acetic acid) or both.

2010-12-31 | E-MEXP-2270 | 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