Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genotyping of Leptospira interrogans in clinical samples by target capture sequencing

ABSTRACT: Our data demonstrate the suitability of target capture technology for purifying very low quantities of Leptospira DNA from biological samples where the human genome is in vast excess. This enables deep sequencing of partial Leptospira genomes directly from clinical samples using next generation technologies and genotyping.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Leptospira kirschneri

SUBMITTER: Juliana Pipoli da Fonseca

PROVIDER: E-MTAB-11667 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (HMEC data)

2010-07-27 | GSE23173 | GEO

Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (Eahy1 data)

2010-07-27 | GSE23172 | GEO

Proteomic analysis of extracellular proteins of Leptospira interrogans

Project description:Leptospira, the causative agent of leptospirosis is known to have several proteases with potential to degrade extracellular matrix. However, a multipronged approach to identify, classify, characterize and elucidate their role has not been attempted. In this study, we carried out in-depth proteomic analysis of Triton X-114 fractions of Leptospira interrogans using high-resolution LC-MS/MS.

2022-02-17 | PXD026044 | Pride

Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (HMEC data)

Project description:The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses. The cell line used fhere was a microvascular endothelial line, HMEC (Ades et al, 1992. HMEC-1: establishment of an immortalized human microvascular endothelial cell line. J Invest Dermatol. 99:683-690); due to loss of the original analysis files, only raw data files are provided. Infection times were performed at a multiplicity of infection (# bacteria/endothelial cell) of 10 for either 1 hour or 3 hours, after which RNA was harvested and reverse transcribed. Labeled cDNAs were used to probe HEEBO arrays purchased from Microarrays Inc. (Nashville, TN). In each of three biological replicate experiments, for each time point, three comparisons were made. First, the L. interrogans-infected cells were compared to the L. biflexa-infected cells. Second, the L. Interrogans-infected cells were compared to the uninfected cells. Third, the L. biflexa-infected cells were compared to the uninfected cells. A second endothelial cell line,

2010-07-27 | E-GEOD-23173 | biostudies-arrayexpress

Analysis of the human endothelial cell response to pathogenic Leptospira interrogans vs. non-pathogenic Leptospira biflexa (Eahy1 data)

Project description:The overall goal of these experiments was to determine how human endothelial cells respond to pathogenic Leptospira interrogans. Leptospira interrogans causes leptospirosis, the most widespread zoonotic infection in the world. A hallmark of leptospirosis is widespread endothelial damage, which in severe cases leads to hemorrhage. In these experiments, we infected two endothelial cell lines with pathogenic Leptospira interrogans serovar Canicola strain Ca12-005, and as controls, with the non-pathogenic Leptospira biflexa serovar Patoc strain Pfra. As additional controls, uninfected cells were also included in the analyses. The cell line used was Ea.hy926, a macrovascular line (Edgell, C. J.,et al. 1990. In vitro Cell. & Dev. Biol. 26:1167-1172, and Edgell, C. J., et al. 1983. Proc. Natl. Acad. Sci. 80:3734-3737). Infection times were performed at a multiplicity of infection (# bacteria/endothelial cell) of 10 for either 1 hour or 3 hours, after which RNA was harvested and reverse transcribed. Labeled cDNAs were used to probe HEEBO arrays purchased from Microarrays Inc. (Nashville, TN). In each of three biological replicate experiments, for each time point, three comparisons were made. First, the L. interrogans-infected cells were compared to the L. biflexa-infected cells. Second, the L. Interrogans-infected cells were compared to the uninfected cells. Third, the L. biflexa-infected cells were compared to the uninfected cells. A second endothelial cell line, HMEC (Ades et al, 1992. HMEC-1: establishment of an immortalized human microvascular endothelial cell line. J Invest Dermatol. 99:683-690), which is of microvascular origin, was also used; raw data files are provided separately.

2010-07-27 | E-GEOD-23172 | biostudies-arrayexpress

Genome-wide transcriptional start site mapping and sRNA identification in the pathogen Leptospira interrogans

Project description:Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Transcriptional regulation of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30° (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts. Primary TSS (pTSS) was identified for 2,865 genes, accounting for 67% of the total genome. The majority of the TSSs were located between 0 to 10 nucleotides from the translational start site. Comparative dRNA-seq analysis revealed conservation of most pTSS at 30° and 37°C. Promoter prediction algorithms allow the identification of the binding sites of the alternative sigma factor sigma 54. However, other motifs were not identified indicating that Leptospira consensus promoter sequences are inherently different from the E. coli model. RNA sequencing also identified 277 and 226 putative small regulatory RNAs (sRNAs) at 30°C and 37°C, respectively, including 8 validated sRNAs by Northern blots. These results provide the first global view of transcriptional start sites and the repertoire of sRNAs in L. interrogans, and will establish a foundation for future experimental work on gene regulation under various environmental conditions including those in the host.

2017-01-23 | GSE92976 | GEO