U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX475350: GSM1333721: Y. pseudotuberculosis RNA-seq _persistent infection; Yersinia pseudotuberculosis YPIII; RNA-Seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 194.2M spots, 39.2G bases, 24.5Gb downloads

Submitted by: NCBI (GEO)
Study: Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [RNA-seq]
show Abstracthide Abstract
We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections. We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence. Comprehensive analysis of mixed RNA populations from infected tissues revealed that Y. pseudotuberculosis undergoes transcriptional reprogramming with drastic down-regulation of T3SS virulence genes during persistence when the pathogen resides within the cecum. At the persistent stage, the expression pattern in many respects resembles the pattern seen in vitro at 26oC, with for example up-regulation of flagellar genes and invA. These findings are expected to have impact on future rationales to identify suitable bacterial targets for new antibiotics. Other genes that are up-regulated during persistence are genes involved in anaerobiosis, chemotaxis, and protection against oxidative and acidic stress, which indicates the influence of different environmental cues. We found that the Crp/CsrA/RovA regulatory cascades influence the pattern of bacterial gene expression during persistence. Furthermore, arcA, fnr, frdA, and wrbA play critical roles in persistence. Our findings suggest a model for the life cycle of this enteropathogen with reprogramming from a virulent to an adapted phenotype capable of persisting and spreading by fecal shedding. Overall design: Examination of Y. pseudotuberculosis expression in two mouse cecal tissue at early and at persistent infection. Also pure bacterial cultures two at 26C and two 37C. Additionally, the bacterial content of cecal tissue during infections and before infection were analyzed with read mapping on 16SMicrobial NCBI database with non-rRNA-depleted reads.
Sample: Y. pseudotuberculosis RNA-seq _persistent infection
SAMN02650477 • SRS561119 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Tissues are taken from the animal and kept in RNALater (Ambion) at +4C for overnight. Tissues are homogenized with two step homogenization for tissue and cell homogenization with a bead beater. RNA extracted based on Trizol method. RNA libraries for sequencing were prepared using TruSeq RNA kits (Illumina, CA, USA) according to the manufacturer's instructions with the following changes. The RNA samples were EtOH precipitated and subsequent protocols (starting from cDNA synthesis in the Illumina provided protocol) automated using an MBS 1200 pipetting station (Nordiag AB, Sweden). All purification steps and gel-cuts were replaced by the magnetic bead clean-up methods described previously (Borgstrom et al., 2011)
Experiment attributes:
GEO Accession: GSM1333721
Links:
Runs: 2 runs, 194.2M spots, 39.2G bases, 24.5Gb
Run# of Spots# of BasesSizePublished
SRR117545796,794,17119.6G12.2Gb2015-07-22
SRR117545897,439,25019.7G12.3Gb2015-07-22

ID:
655840

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...