Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Arabidopsis wild-type, DUF761-1 knock-out mutant and DUF761-1 overexpression strains

ABSTRACT: Expression data from two weeks old Arabidopsis wild-type (Nössen:NO) and at4g16790 (here renamed DUF761-1) knock-out mutant RATM11-0975-1_H (here named duf761-1); Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing DUF761-1 (at4g16790) plants(here named OE6) Microarray assays can facilitate elucidation of cellular processes and gene network functions in the processes of plant growth and development. To gain further insight into the potential molecular role of the at4g16790 gene (here named DUF761-1), we performed Affymetrix whole-genome microarray analysis (http://www.affymetrix.com/) on Nössen and duf761-1plants, and on Columbia-0 and OE6 plants, to compare their genome-wide expression profiles under 22 °C. The differently expressed genes revealed by transcriptional profiling indicate that DUF761-1 may involve in plant cell wall biology and defense response of Arabidopsis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE97660 | GEO | 2018/06/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptom analyses of Arabidopsis altered meritem program1-32 (amp1-32) mutant as well as wild-type Columbia-0 plants via next-generation sequencing (NGS).

Project description:Purpose:The goals of this study are to compare transcriptome of amp1-32 mutant with that of wild-type Columbia-0 plant and to identify genes whose expression are tightly regualted by AMP1 in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30~53 million sequence reads per sample to the Arabidopsis genome (TAIR10). From the 2 biological replicates, we detected 135 up-regulated genes, and 36 down-regulated genes, in the amp1-32 mutant plant. Conclusions: Our study represents the first detailed analysis of transcriptome of amp1 mutant plants, with biologic replicates. Our results show that AMP1 protein had weak, but significant, effects on transcription of genes important for plant development and responses to stresses.

2017-05-30 | GSE81618 | GEO

Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)

Project description:Purpose: The goals of this study are to compare transcriptome of ldl1ldl2 double mutants with that of wild-type Columbia-0 plants and to identify genes whose expression are tightly regualted by LDL1/LDL2 prtoeins in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and ldl1ldl2 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 27~31 million sequence reads per sample to the Arabidopsis genome (TAIR10). Conclusions: Our results show that LDL1 and LDL2 protein had significant effects on transcription of genes important for plant immune reponses against Pseudomonas infection.

2021-04-04 | GSE171433 | GEO

Expression data from rosette leaves of Arabidopsis thaliana which has formaldehyde tolerance (rmpA/rmpB double transgenic) upon formaldehyde exposure

Project description:Formaldehyde is a toxic volatile organic compound and its mechanism of toxicity to plant has not yet been revealed. This experiment was designed to identify formaldehyde-responsible genes under exposure to low or high concentration of airborne formaldehyde for a short period of time. 7 weeks old Arabidopsis thaliana transformant (ecotype: Columbia) plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light-condition for 150 minutes inside a chamber for formaldehyde exposure. Total RNA was isolated from rosette leaves of exposed plants and was applied to microarray analysis. We investigated into formaldehyde dose response on gene expression of Arabidopsis and tried to understand the toxic mechanisms of formaldehyde using an Affymetrix Arabidopsis genome array ATH-1.

2021-03-31 | GSE20865 | GEO

Expression data from rosette leaves of Arabidopsis thaliana wild type upon formaldehyde exposure

Project description:Formaldehyde is a toxic volatile organic compound and its mechanism of toxicity to plant has not yet been revealed. This experiment was designed to identify formaldehyde-responsible genes under exposure to low or high concentration of airborne formaldehyde for a short period of time. 7-weeks old Arabidopsis thaliana wild type (ecotype: Columbia) plants were exposed to gaseous formaldehyde at 1-2 ppm (low), 14-16 ppm (high), or less than 0.04 ppm (air control) at 24oC under light-condition for 150 minutes inside a chamber for formaldehyde exposure. Total RNA was isolated from rosette leaves of exposed plants and was applied to microarray analysis. We investigated into formaldehyde dose response on gene expression of Arabidopsis and tried to understand the toxic mechanisms of formaldehyde using an Affymetrix Arabidopsis genome array ATH-1.

2021-03-31 | GSE20863 | GEO

Arabidopsis thaliana

Project description:Expression data from two weeks old Arabidopsis wild-type (Columbia-0) and transgenic plant overexpressing NHRGP (at4g16790) plants (OE-N6)

| PRJNA319768 | ENA

Proteomic analysis of fractions of Arabidopsis thaliana proteins captured by immobilized metal affinity chromatography

Project description:Proteins from plant shoot and root tissues were extracted from wild-type Arabidopsis thaliana ecotype Columbia (Col-0). They were enriched on conditioned U(VI)-loaded and U(VI)-free Duolite C467 beads. The enriched proteins were identified and quantified by label-free shotgun proteomics.

2023-02-04 | PXD033354 | Pride

G3P triggered changes in systemic transcriptome

Project description:Goal of this study was to determine changes in transcription profile in mock versus G3P treated plants. Arabidopsis (Col-0 ecotype) plants were infiltrated with petiole exudate, with or without G3P, and distal leaves were sampled 24 h post treatments. Keywords: Glycerol-3-Phosphate, Exudate, Salicylic acid, Arabidopsis, Systemic Acquired Resistance, Defense 3 mock-treated and 3 G3P-treated biological replicates were analyzed (one array each) Total RNA was isolated from four-week-old plants using TRIZOL method. The experiment was carried out in triplicate and a separate group of plants was used for each set. RNA was processed and hybridized to the Affymetric Arabidopsis ATH1 genome array GeneChip following the manufacturers instructions (http://www.affymetrix.com/Auth/ support/downloads/manuals/expression_analysis_technical_manual.pdf <http://www.affymetrix.com/Auth/%20support/downloads/manuals/expression_analysis_technical_manual.pdf> ). All probe sets on the Genechips were assigned hybridization signal above background using Affymetrix Expression Console Software v1.0 (http://www.affymetrix.com/Auth/support/downloads/manuals /expression_console_userguide.pdf <http://www.affymetrix.com/Auth/support/downloads/manuals%20/expression_console_userguide.pdf> ). Data was analyzed using the nonparametric Wilcoxen Rank Sum test. Fold changes are reported as ratios of medians. The P values were calculated individually for each probe set.

2011-03-15 | E-GEOD-26973 | biostudies-arrayexpress

Tissue Type Arrays of Columbia-0

Project description:This experiment has been annotated by TAIR (http://arabidopsis.org). In this experiment, different tissue preparations of wild type Columbia-0 Arabidopsis thaliana plants were hybridized and run on the ATH1 Affymetrix platform. Experimenter name = Chris Somerville Experimenter phone = 650-325-1521 ext203 Experimenter fax = 650-325-6857 Experimenter address = Plant Biology Experimenter address = Carnegie Institution Experimenter address = 260 Panama Street Experimenter address = Stanford Experimenter zip/postal_code = CA 94305-1297 Experimenter country = USA Keywords: organism_part_comparison_design;

2006-08-15 | GSE5533 | GEO

Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts

Project description:The ppi2 mutant introgressed into the Columbia-0 ecotype as previously reported. Doublemutant ppi2xrpn8a was crossed with the above referenced genotypes using heterozygous ppi2 plants. After 2 days of stratification at 4 °C the plants were grown on half-strength Murashige and Skoog (M&S) medium supplemented with 0.8% (w/v) plant agar (Duchefa) and 0.8% (w/v) sucrose under short day conditions.

2020-05-27 | PXD017126 | Pride

spy-3_non treated and dry

Project description:Both wild-type and mutant A. thaliana plants (Arabidopsis thaliana L. ecotype-Columbia) were grown in GM plates for 3 weeks under a 16 h light/8 h dark regimen (40 ± 10 umol photons/m2/s) at 22°C. Dehydration treatment: The 3-week-old plants were grown for 2 h without watering.

2012-04-05 | E-MEXP-3171 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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