Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Basal transcriptome of Arabidopsis amino acid transporter mutants

ABSTRACT: Transcriptomes of Arabidopsis knockout mutants for cationic amino acid transporters (CATs) were assessed under normal growth conditions to determine the disruption to normal metabolism caused by the mutations.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Grace Tan

PROVIDER: E-MTAB-15892 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Arabidopsis thaliana hsc70-1/2/3 triple mutant under salt stress

Project description:HSC70 is the cytosolic isoform of plant HSP70. We have found that HSC70 family proteins bind to the heat shock transcription factor A1s (HsfA1s), which are the master regulators of the heat shock response in plants, and suppress their activity. We additionally found that the triple knock out of HSC70s alters responses of Arabidopsis plants to salt stress. To investigate the role of the HSC70s in salt stress responses, we evaluated the effects of the triple knock out on the transcriptome under salt stress.

2021-12-01 | E-MTAB-8723 | biostudies-arrayexpress

Expression data from wild-type and AtERF73/HRE1 knock-down line under hypoxia in Arabidopsis seedlings

Project description:To mimic natural flooding conditions, we have adopted an “open system” treatment, in which only roots are subjected to hypoxia treatment. Using microarray analysis, we identified a number of AP2/ERF genes in Arabidopsis that are induced at different stages of hypoxia treatment. we performed microarray analysis to compare gene expression profiles of wild-type and AtERF73/HRE1-RNAi20 upon normaxic or hypoxic condition, in which AtERF73/HRE1 expression was severely knocked down. Arabidopsis Affymetrix GeneChip arrays were probed with RNAs isolated from roots of untreated plants (controls) and plants treated with hypoxia for 6 h.

2011-02-24 | E-GEOD-27475 | biostudies-arrayexpress

Plant thermospermine-specific polyamine oxidases have a crucial role in vascular development and stem growth and were acquired from Metazoan(s) at non-vascular plant stage

Project description:Arabidopsis thaliana polyamine oxidase 5 gene (AtPAO5) functions as a thermospermine (T-Spm) oxidase. Aerial growth of its knock-out mutant (Atpao5-2) is significantly repressed by low dose(s) of T-Spm but not by other polyamines. Massive analysis of 3â-cDNA ends (MACE) was performed. Cell wall, lipid and secondary metabolisms were dramatically affected in low dose T-Spm-treated Atpao5-2. Intriguingly Fe-deficient responsive genes and drought stress-induced genes were up-regulated, suggesting that vascular system loses the function. Histological observation showed that vascular system of the joint part between stem and leaves was structurally destroyed. The results indicate that T-Spm homeostasis by a balance of synthesis and catabolism, catalysed by AtPAO5 in Arabidopsis, is important for maintaining vascular system. Phylogenetic analysis showed that PAOs from vascular plants are classified into four clades (I-IV) and AtPAO5 belongs to the clade III. Clade III members show high identity to metazoan PAOs and are not found in non-vascular plants. Furthermore, all the clade III genes are intron-less or contain a single intron whereas the other three clade genes usually contain 7 to 9 introns. The data suggest the occurrence of a horizontal gene transfer of ancestral clade III PAO gene(s) from primitive animals. Fine tuning of T-Spm metabolism is critical for vascular plants and its catabolic gene was acquired from a certain Metazoan to equip the vascular system. 8 Samples analyzed by MACE (Massive Analysis of cDNA ends)

2016-02-22 | E-GEOD-69510 | biostudies-arrayexpress

Transcription profiling of Arabidopsis cells cultures undergoing transdifferentiation

Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Experiment Overall Design: 6 samples

2008-06-14 | E-GEOD-6148 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and WRKY33 mutants after salt stress to identify WRKY33 target genes

Project description:Arabidopsis thaliana, wild-type (Col-0) and a T-DNA insertion mutant of WRKY33 gene(SALK_006603, designated as wrky33-1),were hydroponically cultured for 20 d and treated by 150 mM NaCl for 6 h. Roots were harvested and a QiagenOperon oligonucleotide microarray(v1.0.3) was used to identify differentially expressed genes in wrky33-1 mutant compared to wild-type.

2008-08-01 | E-MEXP-1398 | biostudies-arrayexpress

Transcription profiling of Arabidopsis wild type and T-DNA insertion mutant bhlh92 grown under salt stress conditions

Project description:Arabidopsis (wildtype and T-DNA insertion mutant bhlh92) was hydroponicaly cultured for 20 dand treated with 1/2 x MS supplemented with 150 mM NaCl for 6 h. RNA was extracted from roots of wildtype and bhlh92 mutants. Reverse transcription and microarray hybridization was performed to identify the differentially expressed between wildtype and bhlh92 mutants.

2008-07-01 | E-MEXP-1306 | biostudies-arrayexpress

Transcription profiling of roots from wild type and WRKY25 mutant Arabidopsis plants after salt stress to identify AtWRKY25 target genes

Project description:Arabidopsis thaliana, wild-type (Col-0) and a T-DNA insertion mutant of WRKY25 gene(SAIL_529_B11, designated as wrky25-1),were hydroponically cultured for 20 d and treated with 1/2 x MS supplemented with 150 mM NaCl for 6 h. Roots were harvested and RNA samples were prepared. QiagenOperon oligonucleotide microarray(v1.0.3) was used to identify differentially expressed genes in wrky25-1 mutant compared to wild-type under salt stress treatment. Microarray profilings were performed with three independent biological replicates prepared at separate time.

2008-09-01 | E-MEXP-1429 | biostudies-arrayexpress

Transcription profiling of Arabidopsis seedlings under conditions of salt stress for 6, 24 and 48 hours

Project description:Hydroponic cultured Arabidopis thaliana(ecotype Col-0) seeldings(18 days after germination)were treated with 1/2 X MS supplemented with 150 mM NaCl for 6, 24 and 48h, with roots harvested and pooled for RNA extraction. Control roots (1/2 X MS only)were also harvested at the same time for each time-point. 3 independent biological replicates were prepared for each time-point. Altogether 18 hybridizations including dye flips were performed with Qiagen Operon V1.0.2 26k microarray. Microarray data were analyzed using TIGR TM4 suite.

2006-08-23 | E-MEXP-754 | biostudies-arrayexpress

RNAseq of wt and receptor mutant lines in response to 7 elicitor treatments over a 6-point time course

Project description:The degree to which plants discriminate among elicitors in early transcriptional responses is unknown. To test this, we selected a panel of seven elicitors recognized by the model plant Arabidopsis thaliana. Two-week old Arabidopsis seedlings in liquid culture were treated with each elicitor individually, and tissue flash-frozen at 0, 5, 10, 30, 90, and 180 min post-treatment. As a control, receptor mutants for each elicitor were treated and harvested in parallel with wt plants. The experiment was repeated four times. mRNA was extracted via pulldown of poly-A tail from bulk lysate, and libraries were prepared via tagmentation with custom Tn-5 adapter oligos. Libraries for each experiment were pooled, and sequenced across 2-3 flowcells of a NextSeq500 benchtop sequencer.

2021-01-29 | E-MTAB-9694 | biostudies-arrayexpress

Response of rice treated with glutamine and GS-inhibitors

Project description:lo determine transcriptional response to GS-inhibiting herbicides, RNAseq analysis was perform on rice leaf discs treated with 10mM glutamine, 100uM phosphinothricin, or 5uM methionine sulfoxime for 48h. Treatment was performed by floating leaf discs in MS basal media with no sucrose in the light at 28C.

2025-11-05 | E-MTAB-15888 | 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