RNA-seq of THP-1-derived macrophages infected with R. conorii and R. montanensis (1 hpi) against uninfected cells.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB26458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2538790.fastq.gz | Fastqsanger.gz | |||
| ERR2538791.fastq.gz | Fastqsanger.gz | |||
| ERR2538792.fastq.gz | Fastqsanger.gz | |||
| ERR2538793.fastq.gz | Fastqsanger.gz | |||
| ERR2538794.fastq.gz | Fastqsanger.gz |
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Project description:R. conorii (pathogenic) and R. montanensis (non-pathogenic) display opposite survival versus death phenotypes in macrophage-like cells, respectively. We herein employed a global transcriptomic profiling of host responses to infection (1hpi) of human THP-1 macrophages with R. conorii and R. montanensis. Shortly, total RNA was harvested from uninfected, R. conorii- and R. montanensis-infected THP-1 macrophages, DNA was removed from RNA purification (DNAse treatment), ribosomal RNA was depleted and cDNA libraries were constructed. The samples were sequenced using an Ion Proton V2 chip on Ion Chef Instrument. The programmes Cufflinks and Cuffmerge were used to map transcripts and calculate gene expression, and Cuffdiff was used to calculate which samples had genes, which were statistically significantly differentially expressed between conditions.
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Project description:RNA-seq of THP-1-derived macrophages infected with R. conorii and R. montanensis (1 hpi) against uninfected cells.
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Project description:A comparison was made between the THP-1(Human monocytic leukemia cells - TIB-202; ATCC) transcriptional responses of; (i) uninfected versus Coxiella burnetii NMII infected and (ii) uninfected versus Coxiella burnetii NMII infected THP-1 cells transiently treated with bacteriostatic levels (10μg/ml) of chloramphenicol (CAM). Briefly, infections were initiated and cultured in parallel with uninfected cells. At 48 hours post infection (hpi), media containing CAM (10μg/ml) was added to one set of cells (uninfected and infected THP-1 cells) and culturing was continued. The other set of cells were mock treated with normal media. Total RNA was isolated at 72 hpi from all conditions. Microarrays were performed for both condition sets and the results from each of the two microarrays were compared to define the host genes modulated by de novo C. burnetii NMII protein synthesis.
2010-10-01 | GSE23665 | GEO
Project description:Rickettsia conorii, the causative agent of the MSF is transmitted to humans by the bite of infected ticks Rhipicephalus sanguineus. The skin thus constitutes an important barrier for the entry and propagation of R. conorii. Given this, analysis of the survival strategies used by the bacterium within infected skin is critical for our understanding of rickettsiosis. Here, we report the first genome-wide analysis of R. conorii gene expression from infected human skin biopsies. Our data showed that R. conorii exhibit a striking transcript signature that was remarkably conserved across patients, regardless of genotype. The expression profiles obtained using custom Agilent microarrays were validated by quantitative RT-PCR. Within eschars, approximately 15% (n = 211) of the total predicted R. conorii ORFs appeared differentially expressed. These genes are mostly down-regulated and encode proteins essential for bacterial replication. Some of the strategies displayed by rickettsiae to overcome the host defense barriers, thus avoiding killing, were also pointed out. The observed up-regulation of rickettsial genes associated with DNA repair is likely to correspond to a DNA-damaging agent enriched environment generated by the host cells to eradicate the pathogens. Survival of R. conorii within eschars also involves adaptation to osmotic stress, changes in cell surface proteins and up-regulation of some virulence factors. Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae. On the overall, this work provides some insights on how R. conorii counteracts the host cell attack at the site of inoculation which corresponds to the front line of human host defense against rickettsia diffusion and that resembles to battlefield.
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Project description:We used a microarray covering the whole genome of R. conorii to check if intergenic sequences were found transcribed. We checked the expression signals for probes corresponding to spacers as compared to probes corresponding to Open Reading Frames (ORFs). We got total RNA from R. conorii XTC cultures; we performed cDNA synthesis and then hybridizations. The hybridizations were repeated four times, and data were compared to check the reproducibility.
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Project description:Rickettsia conorii are obligate intracellular bacteria responsible for the Mediterranean spotted fever. Their adaptation to highly divergent environments ranging from the arthropod vector to the human beings is essential to survival and virulence. Through a combination of total RNA purification and random prokaryotic cDNA amplification, we successfully analyzed transcription profiles by microarrays starting from 100 ng of R. conorii RNA. Real-time quantitative PCR results performed on unpurified total RNA was consistent with microarray measurements. Here, from the selected targets spotted on our microarray, we showed that in R. conorii, nutrient stress is accompanied by over-expression of the virB operon. Regulation of these genes could be mediated by the stringent response through ppGpp, consistent with the observed up-regulation of spoT and gmk. Exposure of R. conorii to a nutrient stress paradoxically reduced the expression of both GroEL and its transcriptional regulator RpoH. This shows that the over-expression of this chaperonin is a part of the natural life of intracellular growing rickettsiae. Our findings also evidenced that, unexpectedly, many atypical sequences, including small-size split genes, ORFans genes and highly conserved intergenic regions contains expressed sequences that are differentially regulated. The notable deficiency of transcriptional regulators within R. conorii genome does not reflect its incapability to undergo transcriptional changes but rather the existence of an alternative adaptation strategy. Keywords: Global transcriptional analysis
2006-07-06 | GSE5201 | GEO
Project description:Rickettsia conorii, the causative agent of the MSF is transmitted to humans by the bite of infected ticks Rhipicephalus sanguineus. The skin thus constitutes an important barrier for the entry and propagation of R. conorii. Given this, analysis of the survival strategies used by the bacterium within infected skin is critical for our understanding of rickettsiosis. Here, we report the first genome-wide analysis of R. conorii gene expression from infected human skin biopsies. Our data showed that R. conorii exhibit a striking transcript signature that was remarkably conserved across patients, regardless of genotype. The expression profiles obtained using custom Agilent microarrays were validated by quantitative RT-PCR. Within eschars, approximately 15% (n = 211) of the total predicted R. conorii ORFs appeared differentially expressed. These genes are mostly down-regulated and encode proteins essential for bacterial replication. Some of the strategies displayed by rickettsiae to overcome the host defense barriers, thus avoiding killing, were also pointed out. The observed up-regulation of rickettsial genes associated with DNA repair is likely to correspond to a DNA-damaging agent enriched environment generated by the host cells to eradicate the pathogens. Survival of R. conorii within eschars also involves adaptation to osmotic stress, changes in cell surface proteins and up-regulation of some virulence factors. Interestingly, in contrast to down-regulated transcripts, we noticed that up-regulated ones rather exhibit a small nucleotide size, most of them being exclusive for the spotted fever group rickettsiae. On the overall, this work provides some insights on how R. conorii counteracts the host cell attack at the site of inoculation which corresponds to the front line of human host defense against rickettsia diffusion and that resembles to battlefield. 9 R.conorii clinical isolates from eschars co-hybridized with reference strain R.conorii Strain Malish 7
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Project description:We constructed a small RNA cDNA library, using small RNA fraction with a length of 19-29 bases, and we performed deep sequencing of the cDNA library. R. conorii subsp. conorii strain Malish 7 was cultivated on XTC cells for 3 days at 28M-BM-0C. RNA enriched with small RNA fractions was further extracted and cDNA was synthesized.
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Project description:Rickettsia conorii is the etiologic agent of Mediterranean spotted fever, a re-emerging disease with significant mortality. This obligate, gram-negative intracellular pathogen is transmitted via tick bites, resulting in disseminated vascular endothelial cell infection with vascular leakage. In the infected human, Rickettsia conorii infects endothelial cells, stimulating expression of cytokines and pro-coagulant factors. However, the integrated proteomic response of human endothelial cells to R. conorii infection is not known. In this study, we performed quantitative proteomic profiling of R conorii –infected primary HUVECs vs those stimulated with LPS alone.
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