Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18344424.fastq.gz | Fastqsanger.gz | |||
| SRR18344425.fastq.gz | Fastqsanger.gz | |||
| SRR18344426.fastq.gz | Fastqsanger.gz | |||
| SRR18344427.fastq.gz | Fastqsanger.gz | |||
| SRR18344428.fastq.gz | Fastqsanger.gz |
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Project description:Differential RNA-Seq data for Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi)
2024-07-15 | GSE182898 | GEO
Project description:Objectives: determination of transcription start sites in Vibrio harveyi genome and discovery of new transcripts Methods: we performed differential seqencing of total RNA isolated from o.n. control Vibrio harveyi cultures. Sample treatment with Terminator EXonuclease (TEX) allowed differenciation of primary and secondary transcripts, helping in the definition of transcription start sites (TSS) Results: by data-mining RNA-seq data and performing some Northern Blot experiments we were able to detect new putative small-RNAs, along with these results, a more deep analisys of our RNA-seq data will give futher insight into genetic organization of Vibrio harveyi genome to help in its investigation
2018-03-27 | GSE105060 | GEO
Project description:In this research, we used RNA-sequencing technology to detect genome-wide differentially expressed genes in spleen and gill of Vibrio harveyi -infected Takifugu rubripes.This high-throughput sequencing could help us to understand new mechanisms of action of V. harveyi induced aquaculture fish disease.
2022-02-23 | GSE155911 | GEO
Project description:Vibrio harveyi is a major bacterial pathogen that can cause fatal vibriosis in Chinese tongue sole (Cynoglossus semilaevis). To comprehend the molecular mechanisms of C. semilaevis host response against V. harveyi infection, we performed transcriptome (RNA-seq) analysis of C. semilaevis from resistant family and susceptible family.
2019-02-26 | GSE126995 | GEO
Project description:Vibrio species represent one of the most diverse genera of marine bacteria known for their ubiquitous presence in natural aquatic systems. Several members of this genus including Vibrio harveyi are receiving increasing attention lately because they are becoming a source of health problems, especially for some marine organisms widely used in sea food industry. To learn about adaptation changes triggered by V. harveyi during its long-term persistence at elevated temperatures, we studied adaptation of this marine bacterium in sea water microcosms at 30 oC that closely mimicks the upper limits of sea surface temperatures recorded around the globe.
2019-02-05 | GSE113564 | GEO
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains BB721 and JAF548 were hybridized to Agilent arrays (Amadid design ID: 037644), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-08 | E-GEOD-44153 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains STR416 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44197 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains STR415 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44199 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains KM808 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44198 | biostudies-arrayexpress
Project description:We report the application of Solexa/Illumina's digital gene expression (DGE) sequencing approaches to investigate inactivated Vibrio harveyi--induced transcriptome changes in Lateolabrax japonicas, a non model vertebrate species. Totally 3.44 and 3.22 million raw tags were measured. Then, gene annotation was performed by tags mapping analysis and the 169,950 non-redundant consensus sequences from RNA-seq based transcriptome analysis were used as reference transcript database. Tag mapping indicated that Vibrio harveyi--challenged adult Lateolabrax japonicas express over 70% of all genes represented in transcript databases. Meanwhile, totally 1224 consensus sequences exhibited significant difference after the bacterial challenge, in which 1183 transcripts can be well annotated, while approximately 41 transcripts have low sequence homology to the existing known sequences in public databases, suggesting that they might be putative novel immune-relevant genes in Lateolabrax japonicus closely related to the immunity for bacterial challenge. Our present study would greatly benefit to give deep insight into the immunogenetics in fish species, and clinical application in fish diseases. Examination of differentially expressed transcripts in baterial- and mock challenged fish.
2011-06-12 | E-GEOD-21712 | biostudies-arrayexpress