Research
Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays
1 Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montréal, Québec, H4P 2R2, Canada
2 Department of Anatomy and Cell Biology, McGill University, 3640 University Street, Montréal, Québec, H3A 1B1, Canada
3 Department of Biology, McGill University, 1205 Docteur Penfield, Montréal, Québec, H3A 1B1, Canada
4 Intracellular Signaling Laboratory, Institute of Research in Immunology and Cancer (IRIC), University of Montreal, 2900 boulevard Édouard-Montpetit, Montreal, Quebec, H3C 3J7, Canada
5 Department of Molecular Biology and Microbiology, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
Genome Biology 2010, 11:R71 doi:10.1186/gb-2010-11-7-r71
Published: 9 July 2010Additional files
Additional file 1:
Figure S1. GO analysis of the 28% of nuclear genes not expressed in this study.
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Additional file 2:
Table S1. Genome-scale detection of unannotated transcribed segments in C. albicans growing in different conditions.
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Additional file 3:
Table S15. List of nested or overlapping genes validated in this work.
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Additional file 4:
Table S2. List of detected ORFs and pseudogenes.
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Additional file 5:
Table S3. List of ORFs exhibiting long 5' and 3' UTRs (>240 bp)
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Additional file 6:
Table S4. Gene Ontology analysis of ORFs with long 5' and 3' UTR regions (>330 bp).
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Additional file 7:
Tables S5, S6, and S7. Genome-wide detection of ncRNAs: Table S5, AS transcripts; Table S6, housekeeping ncRNAs; and Table S7, RT-qPCR validation of randomly selected ncRNAs.
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Additional file 8:
Figure S2. Transcription and RNAP I and III occupancies within the rDNA locus.
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Additional file 9:
Tables S8 and S9. Detection of RNAP III binding peaks (Table S8) and genomic organization and coordinates of telomeric ncRNA (TelRs; Table S9).
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Additional file 10:
Figure S3. Transcription and RNAP III occupancy of ncRNAs. tRNAs (a, b), RPR1 (b) and an unknown ncRNA (c) are represented.
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Additional file 11:
Table S10. GO process annotation of differentially regulated annotated features using the CGD GO Term Finder [27].
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Additional file 12:
Table S11. List of differentially expressed ORFs in hyphae, biofilm and caecum-grown cells.
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Additional file 13:
Figure S4. Real-time quantitative PCR validation of candidate genes differentially expressed in caecum-grown Candida cells. Both heme-binding (a) and carbohydrate catabolism genes (b) were considered.
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Additional file 14:
Table S12. Genome-scale detection of differentially expressed unannotated transfrags in C. albicans.
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Additional file 15:
Table S13. C. albicans strains used in the study [87,88].
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Additional file 16:
Table S14. Primers used in this study.
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