Open Access Highly Accessed Research article

Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis

Alessandro Guida1, Claudia Lindstädt2, Sarah L Maguire2, Chen Ding23, Desmond G Higgins1, Nicola J Corton4, Matthew Berriman4 and Geraldine Butler2*

Author Affiliations

1 School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

2 School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

3 Department of Pharmacology and Cancer Biology, Duke University Medical Center, Box 3813 Research Drive, Durham, North Carolina, USA

4 Pathogen Genomics Group, Wellcome Trust Sanger Institute, Cambridge, UK

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BMC Genomics 2011, 12:628  doi:10.1186/1471-2164-12-628

Published: 22 December 2011

Additional files

Additional file 1:

Experimental conditions used for RNA-seq analysis. List of conditions used in RNA-seq experiments.

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Additional file 2:

Analysis of UTR regions in C. parapsilosis genes. Table showing the results of the UTR discovery analysis.

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Additional file 3:

GO term enrichment analysis of genes with 5'UTR longer than 500 bp. GO term enrichment analysis performed on genes with 5' UTR longer than 500 bp.

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Additional file 4:

Identification of introns in C. parapsilosis. File listing all the introns and the gene structure with corresponding coordinates.

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Additional file 5:

Validation of selected introns. The table shows the expected product sizes from genomic DNA and from cDNA, as well as information about the C. albicans orthologs.

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Additional file 6:

Intron consensus sequences and length distribution. (A) Comparison of intron length between C. parapsilosis and C. albicans. (B) Comparison of splice-site conservation between Candida parapsilosis and Candida albicans.

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Additional file 7:

Intron conservation in Candida species. Conservation of introns in four Candida genomes (C. albicans, C. dubliniensis, C. parapsilosis and D. hansenii).

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Additional file 8:

Identification of novel transcriptional active regions (nTARs). Transcribed regions that do not overlap with annotated ORFs and do not appear to encode proteins.

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Additional file 9:

Correlation between data from biological replicates for RNA-seq. (A) Heatmap plot showing the correlation of the raw FPKM from the different RNA-seq conditions. (B) Boxplot of the total FPKM values for each RNA-seq library.

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Additional file 10:

Genes differentially expressed in C. parapsilosis in normoxic versus hypoxic conditions. List of genes differentially expressed in hypoxia versus normoxia from (A) RNA-seq and (B) microarray experiment.

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Additional file 11:

GO term analysis of genes differentially expressed in hypoxia from RNA-seq and microarray profiling. (A) Comparison of enriched GO terms from RNA-seq and microarray profiling (B) GO terms enriched in up-regulated genes from microarrays (C) GO terms enriched in down-regulated genes from microarrays (D) GO terms enriched in down-regulated genes from RNA-seq (E) GO terms enriched in up-regulated genes from RNA-seq.

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Additional file 12:

Generating a gene knockout of UPC2 in C. parapsilosis. Generating a gene knockout of UPC2 in C. parapsilosis.

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Additional file 13:

Genes that are differentially regulated in a C. parapsilosis upc2 deletion in hypoxic conditions, identified by both microarrays and RNA-seq. (A) Gene found to be differentially expressed using RNA-seq (B) Genes differentially expressed using microarrays (C) Genes differentially expressed in both RNA-seq and microarray experiments.

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Additional file 14:

GO term enrichment analysis of genes differentially expressed in an upc2 deletion. A) GO term enrichment analysis of genes down-regulated in an upc2 deletion B) GO term enrichment analysis of genes up-regulated in an upc2 deletion.

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Additional file 15:

Cluster analysis of genes differentially expressed in hypoxia in wildtype and in the upc2 deletion. Hierarchical clustering of differentially expressed genes in wildtype and upc2 deletion of C. parapsilosis grown in hypoxia.

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Additional file 16:

Strains used in this study. List of the strains used in this study.

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Additional file 17:

Oligonucleotide primers. List of oligonucleotide primers used in RT-PCR and to validate constructs and introns.

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