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Expression data from C. elegans (wild type vs. tag-24)

ABSTRACT: To provide insights into the mechanism underlying the enhanced immunity of tag-24/octr-1 animals, we used genome microarrays to find clusters of genes commonly misregulated in tag-24 relative to wild-type animals grown on live P. aeruginosa.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE27867 | GEO | 2011/04/21

SECONDARY ACCESSION(S): PRJNA138015

REPOSITORIES: GEO

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Expression data from C. elegans (wild type vs. tag-24)

Project description:To provide insights into the mechanism underlying the enhanced immunity of tag-24/octr-1 animals, we used genome microarrays to find clusters of genes commonly misregulated in tag-24 relative to wild-type animals grown on live P. aeruginosa. Gravid adult wild-type and tag-24/octr-1 animals were lysed using a solution of sodium hydroxide and bleach (ratio of 5:2), washed and the eggs were synchronized for 22 hours in S basal liquid medium at room temperature. Synchronized L1 larval animals were placed onto NGM plates seeded with E. coli OP50 and grown at 20°C until the animals had reached the L4 larval stage. Animals were collected and washed with M9 buffer before transferring to NGM plates containing P. aeruginosa PA14 for 4 hours at 25°C. After 4 hours, animals were collected and washed with M9 buffer, and RNA was extracted using TRIzol reagent (Invitrogen). Residual genomic DNA was removed by DNase treatment (Ambion Austin, TX).

2011-04-21 | E-GEOD-27867 | biostudies-arrayexpress

RNA sequencing to identify UNC-49-regulated genes in C. elegans defense against pathogen P. aeruginosa infection

Project description:Purpose: To gain molecular insights on how UNC-49 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-49(e407) animals relative to wild-type animals with or without P. aeruginosa (PA14) infection. Methods: Synchronized L1 worms were placed onto NGM plates seeded with E. coli OP50 and grown at 20 °C until the L4 stage. Worms were washed off the plates, collected with M9 solution and subsequently transferred to modified NGM plates containing E. coli OP50 or P. aeruginosa PA14 for 24 h at 25 °C. Then, the animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01, China) with liquid nitrogen. Total RNA was isolated using a TransZol Up Plus RNA kit (Transgen, ER501-01, China). Results: RNA seq analyses shows enriched and signficant changed immune genes and pathways that are dependent of GABAergic neuromuscular junctions. Conclusion: Our studies uncover that lack of UNC-49-mediated suppression in unc-49(e407) animals contributes to their improved survival against P. aeruginosa infection.

2025-02-17 | GSE196933 | GEO

C. elegans gene expression in response to acute Pseudomonas aeruginosa infection (Part 1) and recovery (Part 2) by Neomycin/Streptomycin treatment

Project description:(Part 1) Gene expression profiles of C. elegans in response to P. aeruginosa. Synchronized larval stage 1 (L1) worms were raised on E. coli OP50 for 72 hours. These synchronized young adult (YA) animals were subsequently exposed to P. aeruginosa PA14 for 4 hours. 25dC. (Part 2) Gene expression profiles of C. elegans in response to Neomycin/Streptomycin-mediated recovery after a 4 hour exposure to P. aeruginosa. Synchronized larval stage 1 (L1) worms were raised on E. coli OP50 for 72 hours. These synchronized young adult (YA) animals were subsequently exposed to P. aeruginosa PA14 for 4 hours and then treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6, 12, or 24 hours to resolve the infection. As a control for Neomycin/Streptomycin exposure, synchronized larval stage 1 (L1) worms were raised on E. coli OP50 for 72 hours and either shifted to fresh E. coli OP50 plates for 6 hours or treated with Neomycin and shifted to E. coli OP50 plus Streptomycin plates for 6 hours. 25dC.

2016-08-11 | GSE81592 | GEO

Stimulation of Host Immune Defenses by a Small Molecule Protects C. elegans from Bacterial Infection

Project description:The nematode Caenorhabditis elegans offers currently untapped potential for carrying out high-throughput, live-animal screens of low molecular weight compound libraries to identify molecules that target a variety of cellular processes. We previously used a bacterial infection assay in C. elegans to identify 119 compounds that affect host-microbe interactions among 37,214 tested. We subsequently found that one of these small molecules, RPW-24, protects C. elegans from bacterial infection by stimulating the host immune response of the nematode. Using transcriptome profiling, epistasis pathway analyses with C. elegans mutants, and an RNAi screen, we showed that RPW-24 promotes resistance to Pseudomonas aeruginosa infection by inducing the transcription of a remarkably small number of C. elegans genes (~1.3% of all genes) in a manner that partially depends on the evolutionarily-conserved p38 MAP kinase pathway and the transcription factor ATF-7. These data demonstrated that the immunostimulatory activity of RPW-24 is required for its efficacy and define a novel C. elegans-based strategy to identify compounds with activity against antibiotic-resistant bacterial pathogens. Here we present the microarray data that were used to define the genes that are differentially regulated in wild-type nematodes following exposure to RPW-24. There are six samples total that comprise three biological replicates of wild-type animals exposed to either 70 uM RPW-24 or DMSO for 15 hours at 15ﾰC. For a given biological replicate, N2 C. elegans animals in the late L4 larval stage were exposed to RPW-24 or DMSO in parallel to each other.

2012-04-13 | E-GEOD-37266 | biostudies-arrayexpress

RNA sequencing to identify UNC-25-regulated genes in C. elegans defense against pathogen P. aeruginosa infection

Project description:Purpose: To gain molecular insights on how UNC-25 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-25(e156) animals relative to wild-type animals with or without P. aeruginosa (PA14) infection. Methods: Synchronized L1 worms were placed onto NGM plates seeded with E. coli OP50 and grown at 20 °C until the L4 stage. Worms were washed off the plates, collected with M9 solution and subsequently transferred to modified NGM plates containing E. coli OP50 or P. aeruginosa PA14 for 24 h at 25 °C. Then, the animals were washed off the plates with M9 solution and frozen in TRIzol (Transgen, ER501-01, China) with liquid nitrogen. Total RNA was isolated using a TransZol Up Plus RNA kit (Transgen, ER501-01, China). Results: RNA seq analyses shows enriched and signficant changed immune genes, neuropeptides, transcription factors and pathways that are dependent of GABA signaling. Conclusion: Our studies uncover that GABA signaling enhance the resistence to pathogen induced killing.

2023-06-26 | GSE195835 | GEO

Response of C. elegans immune pathway mutants to P. aeruginosa infection

Project description:Synchronized C. elegans cultures of three geontypes -- wildype N2, daf-2(e1370) and sma-6(wk7) -- were prepared using standard techniques (http://cmgm.stanford.edu/~kimlab/index_methods.html). Live young adult worms were split between NG plates pre-seeded with the non-pathogenic E. coli strain OP50 or the Pseudomonas aeruginosa clinical isolate PA14 and incubated at 25C for 4 or 24 hours before harvesting. This experiment was repeated at least three times on independent occasions. cDNA probes were prepared from experimental samples and from reference mRNA extracted from mixed stage wild type worms grown at 25C, and were labeled with Cy3 or Cy5, as indicated. A reference experiement design type is where all samples are compared to a common reference. Elapsed Time: Time Infection: Exposure to the non-pathogenic E. coli strain OP50 or to the pathogenic Pseudomonas aeruginosa strain PA14 Strain Name: C. elegans wildtype strain N2 or the immune pathway mutants daf-2(e1370) or sma-6(wk7) Keywords: reference_design

2008-11-06 | GSE13473 | GEO

Identification of transcription start sites in Streptomyces venezuelae at 10, 14, 18 and, 24 hours of culture by 5' tag RACE.

Project description:Identification of transcription start sites in Streptomyces venezuelae genome after 10, 14, 18 and, 24 hours of culture 5' tag RACE. The 4 time points correspond to late vegetative growth, initiation of sporulation, maturation of spores and, completion of sporulation.

2021-07-09 | E-MTAB-10690 | biostudies-arrayexpress

Caenorhabditis elegans

Project description:Expression data from C. elegans (wild type vs. tag-24)

| PRJNA138015 | ENA

5â-tag sequencing analysis of mouse mitotic chromosome RNA

Project description:As one of the most commonly recognized sub-cellular structures, mitotic chromosome structure and assembly is still lacking. Except the identified proteins and well known genomic composition, the identified mitotic chromosome RNA species is limited. We used a targeted protocol based on 5â-tag sequencing to profile mouse 3T3 cell mitotic chromosome associated RNA composition.

2016-08-05 | E-MTAB-3810 | biostudies-arrayexpress

RNA sequencing to identify UNC-49-regulated genes in C. elegans defense against pathogen infection

Project description:To gain molecular insights on how UNC-49 regulates C. elegans innate immunity, we used RNA sequencing to profile gene expression in unc-49(e407) animals relative to wild-type animals with or without P. aeruginosa(PA14) infection. We found that UNC-49 suppresses the expression of insulin pathway genes, and lack of UNC-49-mediated suppression in unc-49(e407) animals contributes to their improved survival against P. aeruginosa infection.

2023-10-23 | GSE146406 | GEO

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