Ontology highlight
ABSTRACT:
PROVIDER: PRJNA989132 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25070402_1.fastq.gz | Fastqsanger.gz | |||
| SRR25070402_2.fastq.gz | Fastqsanger.gz | |||
| SRR25070403_1.fastq.gz | Fastqsanger.gz | |||
| SRR25070403_2.fastq.gz | Fastqsanger.gz | |||
| SRR25070404_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 186 |
Similar Datasets
Project description:Humans and animals encounter a summation of exposures during their lifetime (the exposome). In recent years, the scope of the exposome has begun to include microplastics. Microplastics (MPs) have increasingly been found in locations where there could be an interaction with Salmonella enterica Typhimurium, one of the commonly isolated serovars from processed chicken. In this study, the microbiota response to a 24-hour co-exposure to Salmonella enterica Typhimurium and/or low-density polyethylene (PE) microplastics in an in vitro broiler cecal model was determined using 16S rRNA amplicon sequencing (Illumina) and untargeted metabolomics. Community sequencing results indicated that PE fiber with and without S. Typhimurium yielded a lower Firmicutes/Bacteroides ratio compared to other treatment groups, which is associated with poor gut health, and overall had greater changes to the cecal microbial community composition. However, changes in the total metabolome were primarily driven by the presence of S. Typhimurium. Additionally, the co-exposure to PE Fiber and S. Typhimurium caused greater cecal microbial community and metabolome changes than either exposure alone. Our results indicate that polymer shape is an important factor in effects resulting from exposure. It also demonstrates that microplastic-pathogen interactions cause metabolic alterations to the chicken cecal microbiome in an in vitro chicken cecal model.
2024-07-08 | MTBLS9001 | MetaboLights
Project description:Comparison of gene expression profiles between two Fayoumi chicken lines, which show a difference in disease resistance to coccidiosis, using our avian intestinal intraepithelial lymphocyte microarray (AVIELA)
2009-04-03 | E-MEXP-1983 | biostudies-arrayexpress
Project description:Chicken 60-mer oligonucleotide microarray, including 39854 cDNA and ESTs, entire Marek’s disease virus and avian influenza virus genomes, and 150 chicken microRNAs, was developed. Cecal tonsil, ileum, liver and spleen from 6 chickens were selected for hybridization to validate the microarray performance. There are 2886, 2886, 2660, 358, 3208 3355, and 3710 genes significantly expressed between liver and spleen, spleen and cecal tonsil, cecal tonsil and ileum, liver and cecal tonsil, liver and ileum, spleen and ileum at the P<10-7. Number of tissue specific genes for cecal tonsil, ileum, liver and spleen was 95, 71, 535, and 108, respectively with p < 10-7. More than 95% of spots had high SNR (>10). Keywords: characteristics of newly developed microarray using different normal tissue
2008-02-29 | GSE7452 | GEO
Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds. Infected, uninfected chicken cecal epithelia and merozoites were selected for RNA extraction and hybridization with Affymetrix microarrays. Our goal was to analyze global transcriptome changes in chicken cecal mucous membranes in response to E. tenella infection in vivo. We used infected (T1,T2,T3; three biological replicates) and uninfected (Neg1, Neg2, Neg3; three biological replicates) samples to identify genes that were differentially expressed. Meanwhile, RNA and probes were also prepared from parasite merozoites (Mzt) from infected samples (Mzt) and used as an additional control in microarray hybridization.
2012-12-10 | E-GEOD-39602 | biostudies-arrayexpress
Project description:An ex vivo system was developed to monitor Salmonella growth, virulence (SPI1 expression) and gene expression (measured by microarray) in response to the permissive and exclusive communities. Yellow fluorescent protein (yfp) and cyan fluorescent protein (cfp) variants were fused to the rrn growth-dependent promoter and the hilA operon (SPI-1 cell invasion locus), respectively, in Salmonella. Fluorescence associated with the YFP and CFP reporters was used to monitor Salmonella growth and SPI1 virulence gene expression in co-culture with cecal communities ex vivo. The Salmonella reporter strain was grown in dialysis tubing in a simulated cecal medium, ex vivo cecal contents (EVCC), submerged in permissive or exclusive communities, to enable collection of Salmonella cells for study. Initially, the fluorescent reporters were used to empirically determine the earliest time point at which the exclusive community had the most significant impact on Salmonella growth or virulence expression relative to the permissive community, which was six-hour co-culture of the reporter strain with the communities. Cells were harvested at that time point for gene expression comparisons. Genes within metabolic pathways that were differentially expressed in permissive vs. exclusive communities were subsequently deleted in Salmonella and mutants’ growth dynamics when cocultured with the exclusive community were monitored over 48 hours using a fluorescence plate reader.
2024-03-25 | GSE261480 | GEO