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ChIP-seq of Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation

ABSTRACT: ChIP-seq of Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation

PROVIDER: PRJNA675635 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13012272.fastq.gz	Fastqsanger.gz
	SRR13012273.fastq.gz	Fastqsanger.gz
	SRR13012274.fastq.gz	Fastqsanger.gz
	SRR13012275.fastq.gz	Fastqsanger.gz
	SRR13012276.fastq.gz	Fastqsanger.gz

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ChIP-seq of Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation

Project description:The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation. C. albicans or C. dubliniensis Ndt80 was tagged with a c-myc epitope in a C. albicans x C. dubliniensis hybrid and the immunoprecipitation of the tagged strain was compared to that of an untagged control hybrid strain.

2021-04-14 | GSE161134 | GEO

ChIP-seq of Ndt80 in a C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different media

Project description:The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different growth media. Ndt80 was tagged with a c-myc epitope in the three species and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain in two different media for each species.

2021-04-14 | GSE161136 | GEO

Comparative Genome Hybridization between Candida albicans and Candida dubliniensis and their derivatives

Project description:Total genomic DNAs of J118, CdUM4b, the pseudotetraploid hybrid strain HBT1 and the progeny hybrid strain HBP1 were isolated. In an attempt to determine the number of copies of individual chromosomes, we used comparative genome hybridization (CGH) analysis using specially designed whole genome microarrays representing C. albicans and C. dubliniensis genomes. The arrays contained 60 mer probes that fell in three categories either C. albicans specific or C. dubliniensis specific or common to both. The specific probes were expected to work as internal controls when hybridized to parental genomic DNA alone. The arrays were individually hybridized to Cy3-labeled genomic DNA from either of C. albicans (J118), C. dubliniensis (CdUM4b) parents or the somatic psudotetraploid hybrid strain, HBT1 and the pseudodiploid progeny hybrid HBP1. After experimentally determining species-specific probes and common probes, the ratios of intensity on the HBT1 hybrid array to those of either of the parents were calculated. The copy number was determined for the entire chromosomes by comparing individual probe intensities from the pseudotetraploid to either diploid parent genome DNA intensities.

2010-12-31 | GSE24269 | GEO

ChIP-seq of biofilm master regulators in four species of Candida

Project description:The purpose of this experiment was to identify the genes bound by the biofilm master regulators (Bcr1, Brg1, Efg1, Ndt80, Rob1 and Tec2) in Candida albicans, C. dubliniensis, C. tropicalis and C. parapsilosis during biofilm formation. The regulators were tagged with a c-myc epitope and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain.

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Comparative Genome Hybridization between Candida albicans and Candida dubliniensis and their derivatives

Project description:Total genomic DNAs of CAKS20, CdUM4b, the pseudotetraploid hybrid strain CACD1 and the progeny hybrid strain Pre3 were isolated. In an attempt to determine the number of copies of individual chromosomes, we used comparative genome hybridization (CGH) analysis using specially designed whole genome microarrays representing C. albicans and C. dubliniensis genomes. The arrays contained 60 mer probes that fell in three categories either C. albicans specific or C. dubliniensis specific or common to both. The specific probes were expected to work as internal controls when hybridized to parental genomic DNA alone. The arrays were individually hybridized to Cy3-labeled genomic DNA from either of C. albicans (CAKS20), C. dubliniensis (CdUM4b) parents or the somatic psudotetraploid hybrid strain, CACD1 and the pseudodiploid progeny hybrid Pre3. After experimentally determining species-specific probes and common probes, the ratios of intensity on the CACD1 hybrid array to those of either of the parents were calculated. The copy number was determined for the entire chromosomes by comparing individual probe intensities from the pseudotetraploid to either diploid parent genome DNA intensities. Agilent one-color CGH experiment,Organism: Human ,Agilent-24598 Genotypic designed C.albicans and C. dubliniensis Cross Species CGH Microarray 4x180k , Labeling kit: Agilent Genomic DNA labeling Kit (Part Number: 5190-0453)

2010-12-31 | E-GEOD-24269 | biostudies-arrayexpress

Transcriptional response of Candida dubliniensis during hypha formation and environmental change

Project description:Transcriptional response of Candida dubliniensis during hypha formation and environmental change (temperature, pH, density and nutrients). Transcript profiling of C. dubliniensis identified a core shared transcriptional response with C. albicans during hypha formation and growth at alkaline pH. However, C. albicans expresses several unique hypha-specific genes, including ALS3, HYR1 and SAP4 and 5. Transcript profiling also revealed a novel role for NRG1 in regulating ferric reductases in C. dubliniensis.

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2010-05-16 | E-GEOD-13593 | biostudies-arrayexpress

ChIP-seq of Ndt80 in a C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different media

Project description:ChIP-seq of Ndt80 in a C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different media

| PRJNA675636 | ENA

Species- and condition-specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis

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.

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