Undefined
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB60595 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR11011327_1.fastq.gz | Fastqsanger.gz | |||
| ERR11011327_2.fastq.gz | Fastqsanger.gz | |||
| ERR11011329_1.fastq.gz | Fastqsanger.gz | |||
| ERR11011329_2.fastq.gz | Fastqsanger.gz | |||
| ERR11011330_1.fastq.gz | Fastqsanger.gz |
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Project description:phi 1720a shiga toxin prophage
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Project description:Temperate bacteriophages (prophages) have recently been demonstrated in Campylobacter jejuni. However, what they do there is largely unknown. In the series of studies that are the subject of these submissions we have investigated the relative expression levels of proteins in C. jejuni isolates that differ in the presence or absence of the CJIE1 prophage. At the time of the initial investigations whole genome sequence data were not available for the isolates used, though DNA microarray data indicated that the isolates were very closely related. The overall project was carried out through four separate experiments. The first set of experiments (experiment 1) therefore compared protein expression in 4-plex iTRAQ experiments using three isolates carrying the (previously sequenced) prophage with a fourth isolate that was epidemiologically and genetically related to these isolates but which naturally lacked the CJIE1 prophage. Three replicate experiments were done. These isolates were grown on medium containing blood to obtain optimal growth and determine whether any differences were found. Three replicate experiments were done. However, since these growth conditions may not mimic in vivo growth of the organism the results may not be considered relevant or very interesting. Previous work in the scientific literature indicated that growth on medium lacking blood but containing sodium deoxycholate induced the expression of at least some proteins associated with virulence and provided data thought to be of relevance to the virulence of the bacterium. Therefore two isolates were chosen, one with and one without the CJIE1 prophage. Each of three replicates of a 4-plex iTRAQ experiment compared protein expression of the two isolates (00-2425 and 00-2426) after growth on Mueller-Hinton agar with and without 0.1% sodium deoxycholate. There was pretty good overlap between the proteins expressed in the first two experiments but, because all results were expressed as log2 change values, it was difficult to determine whether the expression of some proteins was completely absent in one or the other isolate. As well, protein expression overall showed quite extensive differences compared with the first experiment that we attributed to the lack of blood in the growth medium; we thought we might be seeing a response to limited iron as well. Finally, the response to the deoxycholate was extensive, and we wished to further explore this phenomenon as a means of determining or verifying what effects were due to the presence of the CJIE1 prophage and which were due to other differences. Further 4-plex iTRAQ experiments compared protein expression for each of isolate after growth on medium containing blood, without blood, without blood plus sodium deoxycholate, and without blood plus 2.5% Oxgall. Comparison of the results for isolate 00-2425 (with the CJIE1 prophage) and 00-2426 (without the prophage) identified a small number of proteins that could not be detected in one or the other isolate and allowed discrimination of the effects of the prophage from the responses to iron limitation and bile salt preparations. This dataset is associated with the first experiment, experiment 1, which compares C. jejuni isolates carrying the CJIE1 prophage (00-2425, 00-2538, 00-2544) with a very closely related isolate lacking the prophage (00-2426)
2014-07-31 | PXD000798 | Pride
Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced ϕCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of ϕCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage.
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Project description:Fungal Volatiles Enable Prophage Induction
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Project description:Modern Microbialites Metagenome
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Project description:Metagenome sequencing of modern dental calculus
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Project description:Regulatory changes are broadly accepted as key drivers of phenotypic divergence. However, identifying regulatory changes that underlie human-specific traits has proven very challenging. Here, we use 63 DNA methylation maps of ancient and present-day humans, as well as of six chimpanzees, to detect differentially methylated regions that emerged in modern humans after the split from Neanderthals and Denisovans. We show that genes affecting the face and vocal tract went through particularly extensive methylation changes. Specifically, we identify widespread hypermethylation in a network of face- and voice-affecting genes (SOX9, ACAN, COL2A1, NFIX and XYLT1). We propose that these repression patterns appeared after the split from Neanderthals and Denisovans, and that they might have played a key role in shaping the modern human face and vocal tract
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Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced M-OM-^UCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of M-OM-^UCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage. Two strains (WT and lysogen) were subjected for RNA-seq analysis with two biological replicates each.
2014-12-22 | E-GEOD-56818 | biostudies-arrayexpress
Project description:Escherichia coli RS218 genome and prophage
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