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Series GSE56091 Query DataSets for GSE56091
Status Public on Mar 30, 2014
Title Characterization of transcriptome dynamics in response to contact with host cells [Phase I In Vitro]
Organisms Candida albicans; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Candida albicans is the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections which are often life threatening. Hematogenously disseminated candidiasis (HDC) has a 47% mortality rate despite current antifungal therapy. An increase in prevalence, as well as an increasing resistance to most of the clinically important antifungal therapies, provides a strong impetus to understand the molecular mechanisms of pathogenesis and the acquisition of drug resistance. This information holds promise to identify novel therapeutic targets. A complete and accurate characterization of how the transcriptome of C. albicans responds to its interaction with cells from the host is an absolute necessity to accomplish this goal.
RNA-seq (deep-sequencing of cDNA) provides an unbiased method to define comprehensively and systematically the transcriptome of an organism. We propose a comprehensive characterization of the C. albicans transcriptome in two different human tissue culture models, using RNA-seq. Such a characterization will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion.
We performed a comprehensive characterization of the C. albicans transcriptome in two different murine models of candidiasis (HDC and oropharyngeal candidiasis (OPC)), and two different human tissue culture models, using RNA-seq. Because the two murine models accurately recapitulate the pathology that is observed in clinical cases of candidiasis, we are confident that gene expression levels will provide an accurate representation of what occurs during the course of an infection in humans. Such a characterization of the in vivo transcriptome will shed unprecedented light on how fungal pathogens sense and respond to the host environment and how the host tissue responds to fungal invasion.
PRJNA86065
 
Overall design Two different strains of C. albicans (SC5314 or WO-1) were used to infect two different types of human tissue culture monolayers (HUVECs or OKF6-TERT2). RNA from the infection mixtures were harvested at 90 minutes, 5 hours and 8 hours post infection. Experiments were performed in biological duplicate.
 
Contributor(s) Filler S, Liu Y
Citation(s) 25858952
BioProject PRJNA86065
Submission date Mar 21, 2014
Last update date May 15, 2019
Contact name Amol Carl Shetty
E-mail(s) ashetty@som.umaryland.edu
Organization name University of Maryland Baltimore
Department Institute for Genome Sciences
Street address 670 W. Baltimore Street, Floor 3
City Baltimore
State/province Maryland
ZIP/Postal code 21201
Country USA
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15645 Illumina HiSeq 2000 (Candida albicans)
GPL18448 Illumina HiSeq 2000 (Candida albicans; Homo sapiens)
Samples (56)
GSM1354888 90m-HUVEC.control-Candida.SC5314.rep1
GSM1354889 90m-HUVEC.infected-Candida.SC5314.rep1
GSM1354890 90m-OKF6.control-Candida.SC5314.rep1
This SubSeries is part of SuperSeries:
GSE56093 Characterization of transcriptome dynamics in response to contact with host cells
Relations
SRA SRP011085

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56091_RAW.tar 15.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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