Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1003656 | ENA |
REPOSITORIES: ENA
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:TMCO1 co-IP elutions and inputs
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Project description:Using Immunoprecipitation (IP) and mass spectrometry analysis, we aimed at identifying the target of a self-made monoclonal antibody to an unknown molecule on the outer membranes of chicken peripheral blood derived mononuclear cells (PBMC).
2020-06-18 | PXD017248 | Pride
Project description:Transgenic Arabidopsis plants (AGO2::HA:AGO2) were treated with either mock (10 mM MgCl2) or Pseudomonas syringae pv. tomato (Pst) expressing avrRpt2 (R2) at a concentration of 2 x 107 cfu/ml for 14 hours. sRNAs associated with AGO1 and AGO2 were co-immunoprecipitated using antibodies against either AGO1 (AGO1-IP), or HA (hemagglutinin) (AGO2-IP). As controls, we also gel-purified the 18-28 nt fraction of the total RNAs from an AGO2 mutant (ago2-1). The co-immunoprecipitated or gel-purified RNAs were cloned and sequenced by Illumina deep sequencing. Examination of AGO-associated sRNAs in pathogen-treated or control plants
2011-05-10 | E-GEOD-26161 | biostudies-arrayexpress
Project description:Purpose:In order to assess the toxicity of AFB1 in chicken liver and the mechanism of curcumin alleviating AFB1-induced liver toxicity in chicken, we established a co-administered model to investigate LncRNA and mRNA profiles of chicken liver. Methods: RNA extracted by Total RNA Extractor (Trizol) was utilized to construct the final library. Libraries were pooled and sequenced on a 150-bp paired-end Illumina HiSeq™ 2000 run. The sequencing data obtained from Illumina Hiseq™ was filtered to get clean reads using Trimmomatic. The reads themselves and their matching reads which length was less than 35nt were removed. Clean reads were aligned to the reference sequence (Gallus_gallus-5.0, NCBI) using HISAT2. Results: Sampling directly from the liver yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 24,883 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-administered (AFB1 and curcumin) and their underlying mechanisms.
2022-04-02 | GSE148014 | GEO
Project description:Aspergillus fumigatus EdeA CO-IP Raw sequence reads
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Project description:Purpose:In order to assess the respiratory toxicity of co-infection in chicken lung, we established a co-infection model to investigate transcriptome profiles of chicken lung. Methods: RNA extracted by Trizol reagent (Invitrogen) was utilized to construct the final library (BGISEQ-500 RNA-Seq Library) based on the manufacturer’s instructions. Library was validated on the Agilent Technologies 2100 bioanalyzer. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis. Whole transcriptome sequencing data was filtered and mapped to Chicken genome (Gallus genome Version 5.0.1 NCBI). DEG-seq method was based on Poisson distribution (Fold Change > 2 and Adjusted P value < 0.001) Results: Sampling directly from the lung yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 18,043 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-infection (MG and E.coli) and their underlying mechanisms.
2019-04-19 | GSE130015 | GEO
Project description:Proteins interacting with METTL3 were pulled down by CO-IP assay and detected by mass spectrometry sequencing. We found that the splicing factor SRSF2 interacts with METTL3.
2023-03-22 | PXD041020 |
Project description:This dataset has been generated to identify promoter regions in the chicken genome to distinguish active and inactive genes. We focussed our analyses on actively transcribed tRNA and mRNAs genes. Chicken liver was cross-linked to capture histone-DNA interactions. Sequencing libraries were prepared from H3K4me3-precipitated DNA and input control.
2021-02-04 | E-MTAB-8106 | biostudies-arrayexpress
Project description:Purpose: Slam protein and RNA co-localize in early drosophila embryos. slam RNA specifically co-immunoprecipitates with its own protein from embryonic lysate as shown by RNA-IP and QRT-PCR. The goal of this study is to survey transcriptome wide (RNA-seq) targets of slam protein and validate the data from qRT–PCR analysis. Methods: RNA-ip was performed for staged embryos (1.5 – 3 h after egg laying) Using slam antibody or GFP binder. RNA profiles in immune-predicates were generated by deep sequencing. Results: Slam RNA specifically co-predicates with slam protein as shown by both next generation sequencing and RT-QPCR. No mRNA of other genes was detected in all independent experiments or showed the averaged enrichment in the same range.
2017-11-06 | GSE99761 | GEO