Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

C. elegans fer-1 mutant gene expression profile

ABSTRACT: In vertebrate muscle, loss of Dysferlin results in the activation of compensatory muscle gene expression, even at pre-pathological stages. We hypothesized that if C. elegans fer-1 is also expressed in muscle, then fer-1 mutant worms might also exhibit compensatory muscle gene expression. To test this hypothesis, we used Affymetrix microarrays to profile gene expression from synchronized wild type and fer-1 mutant adults. To improve the specificity of this approach, we profiled two well characterized loss-of-function fer-1 mutants (hc1ts and hc24ts) and considered genes that changed similarly in both mutants as fer-1-regulated transcripts.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE16753 | GEO | 2009/06/25

SECONDARY ACCESSION(S): PRJNA117459

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of muscle from wild type and fer-1 mutant C. elegans

Project description:In vertebrate muscle, loss of Dysferlin results in the activation of compensatory muscle gene expression, even at pre-pathological stages. We hypothesized that if C. elegans fer-1 is also expressed in muscle, then fer-1 mutant worms might also exhibit compensatory muscle gene expression. To test this hypothesis, we used Affymetrix microarrays to profile gene expression from synchronized wild type and fer-1 mutant adults. To improve the specificity of this approach, we profiled two well characterized loss-of-function fer-1 mutants (hc1ts and hc24ts) and considered genes that changed similarly in both mutants as fer-1-regulated transcripts. Experiment Overall Design: For each genotype, six individual replicates were performed and were hybridized to Affymetrix C. elegans Genechips using the manufacturerâs recommended protocols. The best four preparations (as determined by the overall Pearson Correlation within a genotype) were used for RNA labeling and hybridization.

2009-07-05 | E-GEOD-16753 | biostudies-arrayexpress

TJ411(fer-15(b26)II; age-1(hx542)II) vs. BA713(fer-15(b26)II)

Project description:To identify changes in gene expression in age-1 mutants, we compared expression in fer-15(b26) animals to expression in fer-15(b26); age-1(hx542) mutants. We prepared RNA from young adult fer-15(b26) mutants grown at 25?C (five samples prepared at Stanford University and six samples prepared at the University of Colorado) and young adult fer-15(b26); age-1(hx542) mutants (four samples at Stanford University and six samples at the University of Colorado). Set of arrays that are part of repeated experiments Place of growth: Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye

2008-07-29 | GSE12166 | GEO

TJ411(fer-15(b26)II; age-1(hx542)II) vs. BA713(fer-15(b26)II)

2008-07-29 | E-GEOD-12166 | biostudies-arrayexpress

TJ1081)fer-15(b26)II; daf-16(m26)I) vs. BA713(fer-15(b26)II)

Project description:To identify changes in gene expression in daf-16 mutants, we compared expression in fer-15 young adults to expression in fer-15(b26); daf-16(m26) young adults grown at 25?C. At Stanford University, four samples of fer-15 and five samples of fer-15; daf-16 animals were prepared. At the University of Colorado, seven samples of fer-15 and six samples of fer-15; daf-16 was prepared. Set of arrays that are part of repeated experiments Place of growth: At Stanford vs Colorado Genotype: mutant strains vs wt (N2) mixed stage; some expts are reverse dye (wt in channel 2) Biological Replicate Computed

2008-07-29 | E-GEOD-12167 | biostudies-arrayexpress

TJ1081)fer-15(b26)II; daf-16(m26)I) vs. BA713(fer-15(b26)II)

2008-07-29 | GSE12167 | GEO

Transcriptome analysis of gene expression changes in fer-8 and the parental line

Project description:To reveal transcriptional changes in the fer-8 mutant that could explain the increase in Pseudomonas colonization, we performed transcriptional profiling in both shoots and roots from fer-8 and the parental line. We identified 675 up-regulated genes in the shoots of fer-8 relative to wildtype plants. Surprisingly, we found only 82 up-regulated genes in fer-8 roots relative to the parental line, and there were no significantly enriched GO terms. In contrast, we found that the genes upregulated in shoots were enriched in GO terms related to defense, response to fungi, and JA signaling, consistent with previous reports of JA activation in the shoots of another fer mutant fer-4.

2021-04-21 | GSE167143 | GEO

The LRX-RALF-FER cell wall integrity sensing module controls plant growth and salt stress responses by modulating multiple plant hormones

Project description:Plants have evolved cell wall integrity signaling pathways to maintain cell wall homeostasis during rapid growth and in response to environmental stress. The cell wall leucine-rich repeat extensins LRX3/4/5, the RAPID ALKALINIZATION FACTOR (RALF) peptides RALF22/23, and FERONIA (FER) function as a module to regulate plant growth and salt stress responses via the sense of cell wall integrity. However, the intracellular signaling pathways that mediate the effects of the LRX3/4/5-RALF22/23-FER module are still largely unknown. Here, we report that jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) accumulate constitutively in lrx345 and fer mutants. Blocking JA pathway rescues the retarded growth phenotype of the lrx345 and fer-4 mutants, while disruption of ABA biosynthesis suppresses the salt-hypersensitivity of these mutants. Many salt stress-responsive genes display abnormal expression patterns in the lrx345 and fer-4 mutants, as well as in wild type plants treated with epigallocatechin gallate (EGCG), an inhibitor of pectin methylesterases, suggesting that the cell wall integrity is a critical factor that determines the expression of stress-responsive genes. Production of reactive oxygen species (ROS) is constitutively increased in the lrx345 and fer-4 mutants, and inhibition of ROS accumulation suppresses the salt-hypersensitivity of these mutants. Together, our results suggest that the LRX3/4/5-RALF22/23-FER module controls plant growth and salt stress responses by regulating hormonal homeostasis and ROS accumulation.

2021-07-15 | GSE136268 | GEO

RNA-seq analysis of total RNA from inflorescence stems of Arabidopsis Col-0, ccr-1, fer-4 and ccr-1/fer-4

Project description:A. thaliana lines with reduced lignin content through down-regulation of the lignin biosynthesis enzymes cinnamoyl CoA reductase (CCR) exhibit extensive cell wall remodeling which results in the release of a mixture of pectic oligosaccharide elicitors of pathogenesis-related (PR) protein gene expression through the salicylic acid signaling pathway. Loss of function of FERONIA, a CrRLK1-like subfamily receptor-like kinase resulted in loss of PR-1, -2 and- 5 gene activation in stems of the ccr1/fer-4 double mutant.

2023-03-20 | GSE210734 | GEO

The soil emergence-related transcription factor PIF3 regulates root penetration by interacting with the receptor kinase FER

Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.

2023-12-31 | GSE225299 | GEO

Transcriptome analysis of differentially expressed genes in the feronia (fer-4) mutant

Project description:FERONIA (FER) receptor kinase is a multifunctional regulator controlling myriad plant growth and developmental processes and interactions with the environment. We perform a RNA-seq analysis of genes differentially expressed in fer-4 mutant and observed significant changes of groups of genes previously characterized to be involved in AUXIN, ABA, ethylene and RALF1 signaling. The Results provide insight into the molecular mechanisms of FERONIA participation in regulating peptide and hormone signaling.

2020-06-30 | GSE125468 | GEO

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