Candida albicans
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ABSTRACT:
PROVIDER: PRJNA288950 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of C. albicans ATCC 10231 (RNA-seq) to transcriptome profiling of garlic oil-treated C. albicans ATCC 10231 and to evaluate protocols for optimal high-throughput data analysis Methods:SDB medium, C. albicans cells and garlic oil were added to two separate 50 mL conical flasks. The initial cell concentrations in culture were both 105 CFU/mL. The cultures were incubated in a water bath shaker at 28 ºC with shaking at 150 rpm for 12 h. Garlic oil or PBS buffer were then added to the cultures to make the concentrations of garlic oil arrived at 0 (control) and 1.25 ?l/mL, respectively. The cultures were continuously incubated at the same conditions for 5 h. The cells were then sampled and centrifuged. The cell precipitates in the control and 1.25 ?l/mL garlic oil groups were quickly separately frozen at -80 ºC. Then total RNA were repared from the cell pellets. Results:The RNA sequencing results showed that many genes in C. albicans exposed to garlic oil were differentially expressed. Nearly three thousand genes were differentially expressed, with either an increase or decrease of more than twofold. Most of them were down regulated while a small number were upregulated. Conclusions: Our study indicated that garlic oil induced differential expression of some critical genes, such as genes for cellular response to drugs, oxidation-reduction processes, pathogenesis, and the cellular response to starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, such as oxidative phosphorylation, spliceosome, cell cycle, protein processing in endoplasmic reticulum, pyrimidine metabolism, meiosis, RNA transport, ribosome biogenesis, and RNA degradation. The mRNA profiles of C. albicans ATCC 10231 (ck) and garlic oil-treated C. albicans ATCC 10231 (sample1) were generated by deep sequencing, in one time, using Illumina Higseq 2500.
2015-07-07 | E-GEOD-70524 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of C. albicans ATCC 10231 (RNA-seq) to transcriptome profiling of garlic oil-treated C. albicans ATCC 10231 and to evaluate protocols for optimal high-throughput data analysis Methods:SDB medium, C. albicans cells and garlic oil were added to two separate 50 mL conical flasks. The initial cell concentrations in culture were both 105 CFU/mL. The cultures were incubated in a water bath shaker at 28 ºC with shaking at 150 rpm for 12 h. Garlic oil or PBS buffer were then added to the cultures to make the concentrations of garlic oil arrived at 0 (control) and 1.25 μl/mL, respectively. The cultures were continuously incubated at the same conditions for 5 h. The cells were then sampled and centrifuged. The cell precipitates in the control and 1.25 μl/mL garlic oil groups were quickly separately frozen at -80 ºC. Then total RNA were repared from the cell pellets. Results:The RNA sequencing results showed that many genes in C. albicans exposed to garlic oil were differentially expressed. Nearly three thousand genes were differentially expressed, with either an increase or decrease of more than twofold. Most of them were down regulated while a small number were upregulated. Conclusions: Our study indicated that garlic oil induced differential expression of some critical genes, such as genes for cellular response to drugs, oxidation-reduction processes, pathogenesis, and the cellular response to starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, such as oxidative phosphorylation, spliceosome, cell cycle, protein processing in endoplasmic reticulum, pyrimidine metabolism, meiosis, RNA transport, ribosome biogenesis, and RNA degradation.
2015-07-07 | GSE70524 | GEO
Project description:Data represents the raw proteomic data generated by SWATH-MS analysis of Candida albicans (ATCC 10231) opaque form cells.
2022-12-31 | MSV000090980 | MassIVE
Project description:Comparative genomic hybridisation between Candida albicans and Candida dublinienis using Eurogentec Candida albicans whole genome microarrays
2004-04-30 | E-MEXP-99 | biostudies-arrayexpress
Project description:Transcriptional profiling of Candida albicans SC5314 comparing C. albicans grown in RPMI1640 or in RPMI1640 with 100ug/ml AAT. Goal was to determine the effects of AAT on global C. albicans gene expression.
2023-01-01 | GSE165326 | GEO
Project description:Transcriptional profiling of Candida albicans cells comparing control untreated C. albicans cells with sulfite-treated C. albicans cells. Sulfite is a toxic molecule that C. albicans encounters in its human host. Both wild type and ∆zcf2 mutant cells were used. The goal was to determine the effects of sulfite on C. albicans gene expression, and to determine which of the genes areZcf2-depedent.
2016-12-03 | GSE90819 | GEO
Project description:Although Candida albicans and Candida dubliniensis are most closely related, both species significantly behave differently with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for C. albicans and C. dubliniensis, respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for C. albicans and C. dubliniensis confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for C. albicans and C. dubliniensis, respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in C. albicans. Species specific adaptation in C. albicans and C. dubliniensis is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level.
2013-04-17 | GSE41749 | GEO