Ontology highlight
ABSTRACT:
PROVIDER: PRJNA625187 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Teladorsagia circumcincta, the brown stomach worm, is the most important gastro-intestinal parasite of sheep in temperate regions and is present on 100% of sheep farms in the UK. Infection with T. circumcincta causes a spectrum of disease in the host, ranging from weight loss to death, and results in significant production losses. Parasitic disease is currently controlled by treatment with anthelmintics but resistance to these drugs is widespread and threatens the viability of the livestock industry. There are now well-documented cases of UK farms harbouring triple-resistant T. circumcincta, which can no longer be controlled by any of the three major anthelmintic classes, forcing farmers to abandon sheep rearing. High-throughput sequencing of life stages of T. circumcincta will be used for gene finding and transcriptome analysis.
2015-06-30 | E-ERAD-342 | biostudies-arrayexpress
Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.
2024-08-04 | GSE273456 | GEO
Project description:NDM-5-harbouring Escherichia coli from a pet dog, UK
| PRJNA473397 | ENA
Project description:To test whether the addition of a peptide nucleic acid (PNA) clamp, which binds WT KRAS at codon 12, can increase the efficacy of mutation detection for KRASG12D within a targeted NGS setting. We tested the effect of clamping the wild-type KRAS sequence in a reference standard (Tru-Q 7, 1.3% Tier from Horizon Diagnostics, Cambridge, UK) with a KRAS c.35G>A mutation (KRASG12D) at an allelic frequency (AF) of 1.3% assessed by digital droplet PCR (ddPCR). We then re-tested the PNA on circulating-free DNA from a patient harbouring a KRASG12D mutation (at an AF of 3.2%, determined by ddPCR). Multiple runs were conducted using 10, 5, 2.5 and 1ng of DNA input.
2017-07-29 | E-MTAB-5718 | biostudies-arrayexpress
Project description:To gain further molecular insight into the observed astrocyte functions, we performed RNA-sequencing (RNA-seq) analysis of the differentiated Ctx-NPCs (control), Ctx-astrocytes and VM-astrocytes used in the co-culture and CM experiments. The genes that are differentially expressed (DEGs) in Ctx-astrocytes compared to differentiated Ctx-NPCs (FPKM>1, log2>1) significantly overlapped with DEGs in VM-astrocytes compared to differentiated Ctx-NPCs
2020-10-25 | GSE106216 | GEO