Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Candida

ABSTRACT: Whole genome sequencing of clinical oral yeast isolates

PROVIDER: PRJNA926612 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23500600_1.fastq.gz	Fastqsanger.gz
	SRR23500600_2.fastq.gz	Fastqsanger.gz
	SRR23500700_1.fastq.gz	Fastqsanger.gz
	SRR23500700_2.fastq.gz	Fastqsanger.gz
	SRR23500800_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 572

Similar Datasets

Candida

Project description:Clinical isolates Candida Genome sequencing and assembly

| PRJNA1077920 | ENA

Genomic insights into a clade-specific Candida tropicalis lineage with resistance to azoles and immune evasion traits

Project description:Candida tropicalis is a leading cause of invasive candidiasis in the Asia-Pacific region with reported crude mortality rates exceeding 50%. The rising prevalence of azole-resistant strains presents a significant clinical challenge. We analyzed 1,016 C. tropicalis clinical isolates collected over nine years from 27 hospitals across North India. Fluconazole resistance was detected in 5.1% (n = 52) of isolates, with cross-resistance observed to voriconazole in 55.7% and itraconazole in 44.2% of isolates. Multilocus sequence typing (MLST) analysis of global 1,630 isolates including 208 Indian and whole-genome sequencing of 716 global isolates (139 Indian) confirmed the clonal emergence and persistence of azole-resistant MLST clade 4 strains in Indian hospitals. Phylogenomic analyses identified that Indian azole-resistant lineage was closely related to azole-resistant isolates from mainland China and Taiwan. The underlying mechanism of resistance involved hotspot mutations (Y132F) in the ERG11 gene along with its duplication, overexpression, and twofold high ergosterol content. Comparative transcriptomics of two clinical isolates exhibiting >512 fold difference in fluconazole susceptibility identified upregulation of virulence-associated genes, ALS7 gene (eightfold), SAP7 and SAP9 (1.6- and 2-fold, respectively) in azole-resistant isolate. Furthermore, azole-resistant isolates showed robust biofilm-associated metabolic activity (twofold), reduced β-glucan exposure, and greater survival in both neutrophil and macrophage killing assays. Notably, azole-resistant lineage exhibits several traits associated with adhesion and immune evasion that could possibly enable its spread in healthcare settings and signals the beginning of a greater spread of this clone. The urgent need for continuous genomic surveillance and antifungal stewardship is warranted to mitigate the spread of multidrug-resistant C. tropicalis.

2026-02-23 | GSE309448 | GEO

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

Candida tropicalis

Project description:Whole genome sequencing of Candida tropicalis isolates

| PRJNA604451 | ENA

Ncb2 ChIP-chip on Gu4 (azole susceptible, AS) and Gu5 (azole resistant, AR) cells of Candida albicans using polyclonal antibody

Project description:Comparative analysis of genome wide binding profile of Ncb2 in azole sensitive (AS, Gu4) and azole resistant (AR, Gu5) clinical isolates of Candida albicans. The goal was to study the role of Ncb2 in acquisition of drug resistance by comparing the binding profiles of Ncb2 in both the isolates.

2017-08-01 | GSE76858 | GEO

Transcrptomic analysis of dysplastic oral keratinocytes infected with Fusobacterium polymorphum strains from patients with leukoplakia

Project description:Fusobacterium polymorphum has been implicated in oral squamous cell carcinoma, yet its widespread presence in the oral cavity raises questions about whether different clinical isolates exert distinct effects on host cells. To explore host transcriptional responses, we performed transcriptomic profiling of dysplastic oral keratinocytes (DOK) following exposure to F. polymorphum isolates derived from across the oral epithelial disease spectrum. The host transcriptomic response revealed a broadly shared pro-inflammatory signature across all isolates, regardless of their clinical origin. However, expression of genes and pathways associated with cell proliferation and related signaling processes varied among isolates and correlated with the dysplasia severity of the lesions from which the strains were derived. These findings suggest that while F. polymorphum isolates elicit a common inflammatory response in epithelial cells, variation in host transcriptional programs linked to proliferation may reflect differences in their biological impact.

2026-03-11 | GSE324461 | GEO

Lactate- and hypoxia-induced beta-glucan masking in responding and non-responding Candida albicans clinical isolates

Project description:RNA sequencing was performed on Candida albicans clinical isolates that display normal (isolates: 3560, 3605, 3609, 4108, 4259) or aberrant (isolates: 3534, 3544, 3621, 3636, 4036) beta-glucan masking in response to lactate and hypoxia. Each clinical isolate was grown to exponential phase in GYNB under normoxic conditions and then exposed for 5 h to: (a) 1% lactate; (b) 0% lactate control; (c) hypoxia; or (d) normoxic control. Three independent experiments were performed for each clinical isolate.

2023-09-05 | E-MTAB-10986 | biostudies-arrayexpress

Transcriptional response of an azole-resistant Candida parapsilosis isolate [voriconazole].

Project description:Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of voriconazole. Whole genome microarrays were used to compare the transcriptional response of the voriconizole-resistant and susceptible isolates.

2011-04-18 | GSE27408 | GEO

Transcriptional response of an azole-resistant Candida parapsilosis isolate [posaconazole].

Project description:Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of posaconazole. Whole genome microarrays were used to compare the transcriptional response of the posaconazole-resistant and susceptible isolates.

2011-04-18 | GSE27407 | GEO

Transcriptional response of an azole-resistant Candida parapsilosis isolate [fluconazole].

Project description:Azole resistance was induced in vitro by growth of a susceptible C. parapsilosis isolate in the presence of fluconazole. Whole genome microarrays were used to compare the transcriptional response of the fluconazole-resistant and susceptible isolates.

2011-04-18 | GSE27405 | 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