Description
Expression profiling by high throughput sequencing
Recent studies have shown that the transcriptional landscape of the pleiomorphic fungus Candida albicans is highly dependent upon growth conditions. Here using a dual RNA-seq approach we identified 299 C. albicans and 72 Streptococcus gordonii genes that were either up- or down-regulated specifically as a result of co-culturing these human oral cavity microorganisms. Seventy five C. albicans genes involved in responses to chemical stimuli, regulation, homeostasis, protein modification and cell cycle were statistically (P ≤0.05) upregulated, while 36 genes mainly involved in transport and translation were down-regulated. Upregulation of filamentation-associated TEC1 and FGR42 genes, and of ALS1 adhesin gene, concurred with previous evidence that the C. albicans yeast to hypha transition is promoted by S. gordonii. Increased expression of genes required for arginine biosynthesis in C. albicans was potentially indicative of a novel oxidative stress response. The transcriptional response of S. gordonii to C. albicans was less dramatic, with only eight S. gordonii genes significantly (P ≤0.05) up-regulated ≥ twofold (glpK, rplO, celB, rplN, rplB, rpsE, ciaR, and gat). The expression patterns suggest that signals from S. gordonii cause a positive filamentation response in C. albicans, while S. gordonii appears to be transcriptionally less influenced by C. albicans.
Data processing
Base calling was carried out using CASAVA v1.8.2
Reads were filtered for quality and adapters removed using fastq-mcf with the parameters -q 20 -l 35 -p 15 -m 3
ERCC transcripts were removed by alignment to the ERCC reference using Bowtie v 1.0.0
Remaining reads were aligned to the C. albicans and S. gordonii reference genomes using Tophat v 2.0.8 with the following parameters: -G <gff> --library-type fr-secondstrand -l 10000 -r 50 --mate-std-dev 100 -p 8
Bedtools multicov was used to quantify the number of reads aligned at each annotated feature.
Differential expression comparisons were carried out using DESeq v.1.12.1 with default parameters.
Genome_build: Ca21_C_albicans_SC5314 genome
Genome_build: NC_009785 S gordonii CH1 genome
Supplementary_files_format_and_content: Tab delimited matrix containing the number of reads aligned to each feature in each sample.
Recent studies have shown that the transcriptional landscape of the pleiomorphic fungus Candida albicans is highly dependent upon growth conditions. Here using a dual RNA-seq approach we identified 299 C. albicans and 72 Streptococcus gordonii genes that were either up- or down-regulated specifically as a result of co-culturing these human oral cavity microorganisms. Seventy five C. albicans genes involved in responses to chemical stimuli, regulation, homeostasis, protein modification and cell cycle were statistically (P ≤0.05) upregulated, while 36 genes mainly involved in transport and translation were down-regulated. Upregulation of filamentation-associated TEC1 and FGR42 genes, and of ALS1 adhesin gene, concurred with previous evidence that the C. albicans yeast to hypha transition is promoted by S. gordonii. Increased expression of genes required for arginine biosynthesis in C. albicans was potentially indicative of a novel oxidative stress response. The transcriptional response of S. gordonii to C. albicans was less dramatic, with only eight S. gordonii genes significantly (P ≤0.05) up-regulated ≥ twofold (glpK, rplO, celB, rplN, rplB, rpsE, ciaR, and gat). The expression patterns suggest that signals from S. gordonii cause a positive filamentation response in C. albicans, while S. gordonii appears to be transcriptionally less influenced by C. albicans.
Data processing
Base calling was carried out using CASAVA v1.8.2
Reads were filtered for quality and adapters removed using fastq-mcf with the parameters -q 20 -l 35 -p 15 -m 3
ERCC transcripts were removed by alignment to the ERCC reference using Bowtie v 1.0.0
Remaining reads were aligned to the C. albicans and S. gordonii reference genomes using Tophat v 2.0.8 with the following parameters: -G <gff> --library-type fr-secondstrand -l 10000 -r 50 --mate-std-dev 100 -p 8
Bedtools multicov was used to quantify the number of reads aligned at each annotated feature.
Differential expression comparisons were carried out using DESeq v.1.12.1 with default parameters.
Genome_build: Ca21_C_albicans_SC5314 genome
Genome_build: NC_009785 S gordonii CH1 genome
Supplementary_files_format_and_content: Tab delimited matrix containing the number of reads aligned to each feature in each sample.
| Date made available | 22 Jun 2015 |
|---|---|
| Publisher | GEO |