Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomics analysis of the Bordetella holmesii response to human serum exposure

ABSTRACT: We performed RNA-Seq transcriptomics analyses of the Bordetella holmesii type strain ATCC 51541T under in vitro growth conditions that mimic exposure to the human bloodstream. We sequenced 3 biological replicates of each of the following conditions of exposure to heat-inactivated human serum: 5% serum, 0.5% serum, and a no serum control. RNA-Seq was performed on the Bordetella holmesii type strain ATCC 51541T grown under three conditions: 5% heat-inactivated human serum, 0.5% heat-inactivated human serum, and a no serum control.

ORGANISM(S): Bordetella holmesii

SUBMITTER: Kent Shefchek

PROVIDER: E-GEOD-56290 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Transcriptomics analysis of the Bordetella holmesii response to human serum exposure

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