Open Access Highly Accessed Research article

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

Christian Grumaz1, Stefan Lorenz2, Philip Stevens2, Elena Lindemann2, Ulrike Schöck3, Julia Retey4, Steffen Rupp2 and Kai Sohn2*

Author Affiliations

1 University of Stuttgart, IGVT, Nobelstr. 12 70569, Stuttgart, Germany

2 Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany

3 GATC Biotech, Jakob-Stadler-Platz 7 78467, Konstanz, Germany

4 Genedata, Margarethenstr. 38 4053, Basel, Suisse

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BMC Genomics 2013, 14:212  doi:10.1186/1471-2164-14-212

Published: 2 April 2013

Additional files

Additional file 1: Figure S1:

Experimental design for RNA-Seq of C. albicans and C. dubliniensis. Bar represents 20 μm.

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Additional file 2: Table S:

Mapping statistics.

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Additional file 3: Table S2A-B:

List of annotated genes.

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Additional file 4: Figure S2:

3- and 5-UTR distribution in C. albicans and C. dubliniensis. Only genes with annotated UTRs were taken into account.

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Additional file 5: Table S3A-C:

UTR analyses.

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Additional file 6: Table S4:

List of novel coding genes.

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Additional file 7: Table S5:

Comparison of novel nc nTARs with reference nc nTARs.

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Additional file 8: Figure S2:

Venn diagram of nc nTARs found in our study tested against three reference datasets449 nc nTARs in C. albicans found in this study were compared with three independently generated sets of nc nTARs from Bruno et al. (590 nc nTARs), Sellam et al. (2161 nc nTARs) and Tuch et al. (866 nc nTARs). 121 out of 449 of our defined nc nTARs did not match in no reference set.

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Additional file 9: Table S6A-B:

RFAM and Snoscan results of novel non-coding genes.

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Additional file 10: Table S7A-C:

List of antisense gene pairs.

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Additional file 11: Table S8A-G:

Reciprocal blast results comprising orthologs and species-specific genes.

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Additional file 12: Table S9A-B:

Conservation of species-specific genes across eight further related species.

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Additional file 13: Figure S3A-D:

Conservation of species-specific genes across eight further related species.

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Additional file 14: Figure S4:

Gene length distribution of expressed and non-expressed genes.

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Additional file 15: Table S10A-D:

Quantification and gene expression analyses.

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Additional file 16: Table S11A-F:

GO term enrichment analyses.

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Additional file 17: Figure S5:

Validation of RNA-Seq data by qRT-PCR for 20 genes in C. dubliniensis during yeast to hyphae transition.

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Additional file 18: Table S12:

List of primers used in qRT-PCR.

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