The gene expression of wild-type worms and kin-1(ok338) mutant worms exposing Salmonella entericaSL1344 at 24 hours
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE86342 | GEO | 2017/03/03
SECONDARY ACCESSION(S): PRJNA341485
REPOSITORIES: GEO
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Project description:Investigation of whole genome gene expression level changes in C. elegans genes kin-1 and crh-1 mutant, compared to the wild-type strain. NimbleScan softwareM-bM-^@M-^Ys implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249). A nine chip study using total RNA recovered from three separate wild-type cultures of C. elegans and three separate cultures of kin-1 mutant, and three separate cultures of crh-1 mutant. The C. elegans 12 x 135K Gene Expression Array was manufactured by Roche NimbleGen. This array enables you to conveniently and simultaneously hybridize 12 samples on each slide. About 13,187 genes are collected from the authoritative data source including Wormbase.
2012-09-13 | E-GEOD-40809 | biostudies-arrayexpress
Project description:To clarify the mechanisms of innate immune responses mediated by epithelial barrier disruption. Reveal the host’s broad transcriptional response to P. aeruginosa infection during disruption of the intestinal barrier. We used RNA-Seq analysis to study the transcriptomic profiles of wt worms were exposed to either P. aeruginosa PA14 or E. coli OP50 for 24 hours, and the transcriptomic profiles of egl-44(MT2247) mutants fed E. coli OP50 for 24 hours. Differential expression analysis was performed by comparing wt worms exposed to PA14 versus wt worms exposed to E. coli OP50, and egl-44(MT2247) mutants fed E. coli OP50 versus WT worms fed E. coli OP50.
2018-10-11 | GSE121091 | GEO
Project description:We exposed wild-type Vibrio cholerae E7496, multiple Vibrio cholerae virulence factor deleted genes with intact hemolysin A gene [CVD109] and without hemolysin A gene [CVD110] in E7946, and E.coli OP50 to wild-type C.elegans N2 for 18 hours. We used microarrays to detail the global gene expression and identified distinct classes of up-regulated and down-regulated genes during this process.
2011-12-02 | GSE34026 | GEO
Project description:Investigation of whole genome gene expression level changes in C. elegans genes kin-1 and crh-1 mutant, compared to the wild-type strain. NimbleScan software’s implementation of RMA offers quantile normalization and background correction. There are three steps of RMA: Firstly, background subtraction was performed using a local background estimator. Secondly, quantile normalization (Bioinformatics 2003; 19:185) at probe level was done to make the expression distributions the same for all arrays. Last, probe set summarization was performed using Robust Multichip Average (RMA) algorithm as described by Irizarry, et al. (Nucleic Acids Res. 2003; 31:e15 and Biostatistics 2003; 4:249).
2012-09-13 | GSE40809 | GEO
Project description:Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known. Here we show that treatment of wild-type S49 lymphoma cells for 24 h with 8-(4-chlorophenylthio)-cAMP (CPT-cAMP), a PKA-selective cAMP analog, alters the expression of ~4500 of ~13,600 unique genes. By contrast, gene expression was unaltered in Kin- S49 cells (that lack PKA) incubated with CPT-cAMP. Changes in mRNA and protein expression of several cell-cycle regulators accompanied cAMP-induced G1-phase cell-cycle arrest of wild-type S49 cells. Within 2 h, CPT-cAMP altered expression of 152 genes that contain evolutionarily conserved cAMP-response elements (CRE) within 5 kb of transcriptional start sites, including the circadian clock gene Per1. Thus, cAMP through its activation of PKA produces extensive transcriptional regulation in eukaryotic cells. These transcriptional networks include a primary group of CRE-containing genes and secondary networks that include the circadian clock.
2007-08-31 | E-GEOD-2413 | biostudies-arrayexpress
Project description:We exposed wild-type Vibrio cholerae E7496, multiple Vibrio cholerae virulence factor deleted genes with intact hemolysin A gene [CVD109] and without hemolysin A gene [CVD110] in E7946, and E.coli OP50 to wild-type C.elegans N2 for 18 hours. We used microarrays to detail the global gene expression and identified distinct classes of up-regulated and down-regulated genes during this process. C. elegans were exposed to Vibrio cholerae and E.coli then hybridization on Affymetrix microarray chips.
2011-12-02 | E-GEOD-34026 | biostudies-arrayexpress
Project description:Abstract Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known. Here we show that treatment of wild-type S49 lymphoma cells for 24 h with 8-(4-chlorophenylthio)-cAMP (CPT-cAMP), a PKA-selective cAMP analog, alters the expression of ~4500 of ~13,600 unique genes. By contrast, gene expression was unaltered in Kin– S49 cells (that lack PKA) incubated with CPT-cAMP. Changes in mRNA and protein expression of several cell-cycle regulators accompanied cAMP-induced G1-phase cell-cycle arrest of wild-type S49 cells. Within 2 h, CPT-cAMP altered expression of 152 genes that contain evolutionarily conserved cAMP-response elements (CRE) within 5 kb of transcriptional start sites, including the circadian clock gene Per1. Thus, cAMP through its activation of PKA produces extensive transcriptional regulation in eukaryotic cells. These transcriptional networks include a primary group of CRE-containing genes and secondary networks that include the circadian clock. Keywords: time-course
2005-04-15 | GSE2413 | GEO
Project description:The ability to sense, respond and adapt to changes in nutrient availability is a survival requisite. This might be particularly important for malaria parasites, which encounter major alterations in nutrients levels throughout infection. How these parasites deal with nutrient fluctuations and maintain infection without killing their hosts before transmission remains unknown. Here, we show that blood-stage malaria parasites respond to dietary-restriction through a rearrangement of their transcriptome accompanied by a significant reduction in their multiplication rate. A kinome analysis combined with chemical and genetic approaches identified KIN, a putative AMP-activated kinase homologue, as a master regulator that senses host nutrients both in vitro and in vivo, and mediates the transcriptional response to the host nutritional status. Diet-responsive genes include the plant-like ApiAP2 transcription regulators, which appear to act as downstream effectors of KIN. Overall, these findings reveal key components of a parasite nutrient-sensing mechanism that is critical to modulate replication and virulence in malaria parasites.
2017-07-14 | GSE69627 | GEO
Project description:BioID experiment of KIN protein to determine its interactors
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Project description:Sib mating increase homozygosity and can lead to inbreeding depression. Selective pressures have favored the evolution of kin recognition and sib avoidance in mate choice. Such avoidance behavior has been recorded in the parasitoid wasp Venturia canescens where the sex determining system (single-locus complementary sex determination, sl-csd) introduces an extra short-term cost to inbreeding; females preferentially mate with unrelated males. The genetics underlying mate choice of females and kin recognition remains largely unexplored. Here we analyzed the head transcriptomic changes after exposure to distinct stimulus: courtship by unrelated male or courtship by brother, while transcriptome of females alone was used as control. Our results demonstrate that male courtship provokes a major transcriptome reprogramming in females heads. The transcriptomic response is highly dependent on the compatibility of the courting male. We subdivided the socially responsive genes using an integrative gene network analysis, we highlighted genes regulated by courtship, whatever the relatedness of the courting male. We also showed that the regulation of some peculiar group of genes is very specific of compatible male courtship, while others are regulated only by incompatible male courtship. We suggest that those different transcriptomic responses lead to mating decision or sib mating avoidance behavior observed in this species.
2018-12-20 | GSE124129 | GEO