RNA-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB38562 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed. Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes. In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads. A comparison with the previous microarray data showed good correlation between the shared genes. The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed. Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR. The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics. One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs. The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus. The wild type Vibrio parahaemolyticus BB22 strain LM5312 and an opaR deletion strain LM5674 were analyzed for mRNA expression using RNA-Seq.
2013-12-31 | E-GEOD-53639 | biostudies-arrayexpress
Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a miRNA-seq analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.
2020-06-18 | GSE107696 | GEO
Project description:We report that ChIP-seq analyses of the quorum-sensing regulator OpaR at late-log and stationary phase in Vibrio parahaemolyticus
2020-10-27 | GSE122479 | GEO
Project description:Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed. Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes. In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads. A comparison with the previous microarray data showed good correlation between the shared genes. The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed. Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR. The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics. One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs. The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus.
2013-12-31 | GSE53639 | GEO
Project description:RNA-Seq analysis carried out in three different backcrosses based on Iberian breed with Landrace, Pietrain and Duroc breeds
2017-10-31 | PRJEB23068 | EVA
Project description:In order to gain a better understanding of the impact of Vibrio parahaemolyticus infection on genetic regulation of Litopenaeus vannamei,we performed a transcriptome analysis in the hepatopancreas of Litopenaeus vannamei challenged with Vibrio parahaemolyticus, using the Illumina HiSeq 2500 platform.
2020-06-18 | GSE107697 | GEO
Project description:RNA-seq for WT and WT+Nitrite/Nitrate vibrio parahaemolyticus.
| PRJEB40744 | ENA
Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Vibrio parahaemolyticus wild type strain RIMD 2210633 compared with the mutants of VtrA and VtrB have a winged helix-turn-helix DNA binding motif that genes encoded on pathogenicity island loci, at OD600=1.0 in Luria-Bertani containing medium 0.5 % NaCl at 37˚C. Our goal is to determine the VtrA or VtrB regulon.
2010-07-16 | GSE17242 | GEO
Project description:Elucidation of host-pathogen interaction is essential for developing effective strategies to combat bacterial infection. Dual RNA-Seq using cultured cells or tissues/organs as the pathogen host has emerged as a novel strategy to understand the response concurrently from both pathogen and host at cellular level. However, bacterial infection mostly causes systematic responses from the host at organism level where the interplay is urgently to be understood but inevitably being neglected by the current practice. Here, we developed an approach that simultaneously monitor the genome-wide infection-linked transcriptional alterations in both pathogenic Vibrio parahaemolyticus and the infection host nematode Caenorhabditis elegans. Besides the dynamic alterations in both transcriptomes of C. elegans and V. parahaemolyticus during infection, we identify a two-component system, BarA/UvrY, that are essential for host colonization. BarA/UvrY not only controls the virulence factors in V. parahaemolyticus including Type III and Type VI secretion systems, but also represses the MAP kinase mediated signaling cascades to attenuate innate immune responses. Thus, our study exemplifies the use of dual RNA-Seq at organism level to uncover previously unrecognized interplay between host and pathogen.
2020-09-10 | GSE138199 | GEO