Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome sequencing of Chlamydia isolates from mammals

ABSTRACT: Illumina Miseq genome sequencing of Chlamydia isolates from mammals

PROVIDER: PRJEB25774 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR7801112_1.fastq.gz	Fastqsanger.gz
	ERR7801112_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

Whole genome sequencing of Chlamydia isolates from birds

Project description:Illumina Miseq genome sequencing of Chlamydia isolates from birds

| PRJEB25740 | ENA

Whole Genome Sequencing of a Chlamydia pecorum isolate

Project description:Illumina Miseq genome sequencing of a Chlamydia pecorum isolate from a chamois (PV7855).

| PRJEB25743 | ENA

Transcriptional profiling of human epithelial cells infected with trachoma isolates of Chlamydia trachomatis

Project description:Hep-2C cells were infected with A/2497 or B/Tunis-864 strains of Chlamydia trachomatis to compare changes in host gene expression

2019-12-31 | GSE133358 | GEO

Diversity in gene expression profiles captured through highly resolved whole-transcriptome profiling of clinical and laboratory-adapted malaria parasite isolates

Project description:We present highly replicated whole transcriptome gene expression profiles of schizont-stage malaria parasites using RNA-seq analysis of multiple clinical isolates and laboratory-adapted lines Methods: Transcript profiles of schizont-stage laboratory-adapted and clinical malaria parasite isolates were generated by RNA sequencing. Five to ten replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Paired-end fastQ files were aligned using hisat2 and converted to indexed bam files using samtools. Bam files were filtered to exclude reads with MAPQ scores below 60. Reads were counted using SummarizeOverlaps feature of the GenomicAlignments package in R. Differential expression analysis was conducted using DESeq2 in R. qRT–PCR validation of differentially expressed genes was performed using SYBR Green assays for eight genes. Results: We show that increasing sample replication improves the true-positive discovery rate, and that when fewer replicates are available, focussing on the most highly expressed genes maintains the true-positive discovery rate. We identify schizont-stage genes that appear to alter in expression through the process of culture adaptation, as well as genes that show variable expression between isolates. We extend transcript quantitation for variably expressed genes to an even wider panel of ex vivo clinical isolate samples. Conclusions: Our study represents the first detailed analysis of replicated P. falciparum schizont-stage transcriptomes. Our data show that high levels of replication are necessary to capture gene expression differences among parasite isolates. We identify schizont-stage expressed genes that may be differentially expressed as a mechanism of immune evasion.

2018-04-27 | GSE113718 | GEO

ESGI Whole Genome Sequencing of samples from the Cilentogen isolates

Project description:Deep whole genome sequencing of sampels from the Cilento isolates. The samples are sequenced using the Illumina HiSeq X Ten system.

| EGAS00001001116 | EGA

P.vivax whole genome sequencing

Project description:P. vivax isolates, Illumina sequencing

| PRJEB36199 | ENA

Whole-genome sequencing of ocular Chlamydia trachomatis isolates from Gadarif State, Sudan.

Project description:BACKGROUND:Trachoma, caused by ocular Chlamydia trachomatis, is the leading infectious cause of blindness worldwide. Sudan first reported trachoma in the 1930s and has since been consistently endemic. Ocular C. trachomatis previously isolated from trachoma patients in Sudan in 1963 was antigenically identical to an isolate from Saudi Arabia (A/SA1). No contemporary ocular C. trachomatis whole genome sequences have been reported from Sudan. METHODS:This study sequenced twenty ocular C. trachomatis isolates to improve understanding of pathogen diversity in North-East Africa and examine for genomic variation specific to Sudan, possibly related to the persistence of trachoma in surveyed communities. High quality, whole genome sequences were obtained from 12/20 isolates. RESULTS:All isolates were serovar A and had tarP and trpA sequences typical of classical, ocular C. trachomatis isolates. The Sudanese isolates formed a closely related subclade within the T2-trachoma clade of C. trachomatis phylogeny distinct from geographically disparate ocular isolates, with little intra-population diversity. We found 333 SNPs that were conserved in Sudanese ocular isolates but rare compared to other ocular C. trachomatis populations, which were focused in two genomic loci (CTA0172-CTA0173 and CTA0482). CONCLUSIONS:Limited intra-population diversity and geographical clustering of ocular C. trachomatis suggests minimal transmission between and slow diversification within trachoma-endemic communities. However, diversity may have been higher pre-treatment in these communities. Over-representation of Sudan-specific SNPs in three genes suggests they may have an impact on C. trachomatis growth and transmission in this population.

| S-EPMC6829945 | biostudies-literature

Whole genome sequencing of Burkholderia contaminans sequential isolates

Project description:The data represent whole genome sequencing of two sequential isolates of B. contaminans ST872 that have been retrieved form a cystic fibrosis patient during different phases of chronic pulmonary infection.

2016-05-13 | E-MTAB-4649 | biostudies-arrayexpress

A class II-restricted chlamydia-specific CD8ɣ13 T cell clone protects the genital tract during Chlamydia muridarum infection

Project description:The T cell response to Chlamydia genital tract infections in humans and mice is unusual in that the majority of antigen-specific CD8 T cells are not restricted by HLA/MHC class I and therefore have been referred to as “unrestricted” or “atypical”. We previously reported that a subset of unrestricted murine Chlamydia-specific CD8 T cells had an unusual cytokine polarization pattern that included IFN-ɣ and IL-13. For this report, we investigated the transcriptome of Chlamydia-specific CD8ɣ13 T cells, comparing them to Chlamydia-specific multifunctional Tc1 clones using gene expression micro array analysis. The molecular study revealed that CD8ɣ13 polarization included IL-5 in addition to IFN-γ and IL-13. Adoptive transfer studies were performed with Tc1 clone and CD8ɣ13 T cell clones to determine whether either influenced bacterial clearance or immunopathology during Chlamydia muridarum (Cm) genital tract infections. To our surprise, an adoptively transferred CD8ɣ13 T cell clone was remarkably proficient at preventing chlamydia immunopathology while the multifunctional Tc1 clone did not enhance clearance or significantly protect from immunopathology. Mapping studies with MHC class I- and class II-deficient splenocytes showed our previously published Chlamydia-specific CD8 T cell clones are MHC class II-restricted. MHC class II-restricted CD8 T cells may play important roles in protection from intracellular pathogens that limit class I antigen presentation or deplete the CD4 T cell compartment.

2020-05-21 | GSE140213 | GEO

Human epithelial cell line (HL) infected with Chlamydia pneumoniae

Project description:Transcriptional profiling of human epithelial cell line (HL) infected with Chlamydia penumoniae compared to control cells at time points 12h, 24h, 48h, 72h after the infection. Keywords: Chlamydia peneumoniae infection

2008-03-30 | GSE7246 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data