Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of the Arabidopsis glucosinolate deficient mutants, ref5-1 and ref2-1 and med5 mutants

ABSTRACT: Purpose: To identify changes in gene expression in ref5-1 and ref2-1 compared with wild type and ref5-1 med5 and ref2-1 med5 compared to ref5-1 or ref2-1 respectively Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 71 genes that were differentially expressed in both ref5-1 and ref2-1 compared to wild type but their altered expression is restored.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE99581 | GEO | 2019/06/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression profiling of the Arabidopsis Mediator MED5 mutant ref4-3 and suppressors thereof

Project description:Purpose: To identify changes in gene expression in the ref4-3 mutant that contribute to the mutant’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and suppressors of ref4-3. Methods: Gene expression profiles were generated from 18-day-old, pooled Arabidopsis rosettes in biological quadruplicate, by paired-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 14,688 genes that were differentially expressed across the 10 genotypes (ANOVA, FDR <0.05).

2018-02-16 | GSE95574 | GEO

Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1

Project description:Purpose: To identify changes in gene expression in ref4-3 mutant that contribute to the mutant’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and ref4-3 cdk8-1. Methods: Gene expression profiles were generated from 20-day-old, pooled Arabidopsis rosettes in biological triplicate, by paried-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using TopHat. Gene counts were determined using HTseq-count. Differential expression analysis was performed using edgeR. Results: We identified 7,355 genes that were differentially expressed in ref4-3 compared to wild type, part of which were significantly rescued by loss of CDK8 (FDR <0.05).

2019-02-22 | GSE111290 | GEO

Gene expression profiling of lignin biosynthetic mutants of Arabidopsis

Project description:Purpose: To investigate the global impact of lignin perturbation on transcription in plants, we analyzed transcriptomes from rapidly lignifying stem tissue in wild-type Arabidopsis and 13 selected mutants. Methods: RNA-sequencing was conducted to profile the transcriptome in basal stem tissue of Arabidopsis plants. PolyA+ RNA libraries were constructed and paired-end sequencing was performed on Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using HISAT2. Gene counts were analyzed using HTSeq-count program and differential gene expression using DESeq2. Results: The whole dataset contains 20974 expressed genes and 5581 differentially expressed genes in at least one mutant (ANOVA, FDR < 0.05, Fold change ≥ 2 fold).

2022-07-15 | GSE206323 | GEO

Overexpression of ENOD40 in Arabidopsis thaliana plants reveals a role of the gene in cell wall turnover and glucosinolate accumulation.

Project description:The transcriptional and metabolic profiles of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed. ENOD40 overexpression resulted in 382 modulated genes, 142 of which upregulated and 165 downregulated in all the three transformed lines. Cell wall, membrane, hydrolase activity on glycosidic bonds, defense response and response to stimulus gene categories were overrepresented in the modulated genes compared to TAIR complete database. Metabolomics analysis (through liquid chromatography-mass spectrometry) allowed to putatively identify 13 different glucosinolates, some flavonoids, sinapic and ferulic acid derivatives, hydroxybenzoic acid derivatives, non aromatic organic acids, amino acids. Positive genes biomarkers of the transformed plants were mainly involved in cell wall turnover, whereas positive metabolite biomarkers were the methylthioalkyl-glucosinolates. The transcriptional profile of rosettes of three independent Arabidopsis thaliana ecotype Wassiliewska lines overexpressing the soybean early noduline GmENOD40 gene were compared to those of wt, and a biomarker analysis was performed.

2015-05-08 | E-GEOD-37867 | biostudies-arrayexpress

set2, set2sir4 transcription profiles

Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type Keywords: quadruplicate mutant:WT analysis, with dye-swapping

2006-06-01 | GSE4934 | GEO

set1, H3K4A, set1htz1, set1htz1sir2 transcription profiles

Project description:Relative mRNA abundance of all S. cerevisiae genes was measured in various mutants, compared to wild-type Keywords: quadruplicate mutant:WT analysis, with dye-swapping

2006-05-17 | GSE4826 | GEO

Expression data from Arabidopsis autophagy mutants (atg5 and atg9) and wild type (Col-0)

Project description:Autophagy mutants display early yellowing phenotype and major metabolic changes under both ideal and limiting nitrate supplies. We used Affymetrix microarrays to detail the global programme of gene expression underlying metabolic and cellular changes in autophagy mutants and wild type Arabidopsis rosettes grown under both low or high nitrate conditions. Fold changes data between mutants and wild type have been published (www.plantcell.org/cgi/doi/10.1105/tpc.114.124677)

2021-10-01 | GSE185085 | GEO

Analysis of isolated Plastoglobules from Arabidopsis thaliana WT and M48 null mutants.

Project description:We studied the function of PG localized protease, PGM48 both in vitro and in vivo during natural senescence in Arabidopsis thaliana.Our results show that PGM48 is a metalloprotease and a senescence inducible protein. In vitro assay by recombinant protein revealed a proteolytic activity. Quantitative proteome analysis of PGs from senescing rosettes of overexpression plants lines showed a significantly reduced level of CAROTENOID CLEAVAGE ENZYME 4 ( CCD4) protein but 2-3 fold higher level of phytyl-esterase (PES1) compared to wild type; the opposite results were found in RNAi lines. Yeast-2-hybrid analysis and in vitro pull-down experiments showed that PGM48 interacts with the kinase ABC1K3, PES1 and CCD4, but not with chlorophyll catabolic enzymes. We propose that PGM48 acts as a positive regulator of leaf senescence.

2019-04-09 | PXD003684 | Pride

Overexpression of ENOD40 in Arabidopsis thaliana plants reveals a role of the gene in cell wall turnover and glucosinolate accumulation.

2015-05-08 | GSE37867 | GEO

Expression profiling of the plant cell wall mutants: pmr5, pmr6 and pmr5 pmr6 double mutants

Project description:The rosettes from genotype Col-0, pmr5, pmr6 and pmr5 pmr6 double mutant were collected for RNA expression profiling when the plants were 3 weeks old. Keywords: cell wall mutant

2008-09-01 | GSE9957 | 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