Open Access Highly Accessed Research article

Transcriptional landscape of Aspergillus niger at breaking of conidial dormancy revealed by RNA-sequencing

Michaela Novodvorska1, Kimran Hayer1, Steven T Pullan1, Raymond Wilson2, Martin J Blythe2, Hein Stam3, Malcolm Stratford1 and David B Archer1*

Author Affiliations

1 School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK

2 Deep Sequencing Facility, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK

3 DSM Food Specialties, Research and Development, P.O. Box 1, Delft, 2600 MA, The Netherlands

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BMC Genomics 2013, 14:246  doi:10.1186/1471-2164-14-246

Published: 11 April 2013

Additional files

Additional file 1: Figure S1:

Percentage of detected calls. Percentage of Affymetrix probe sets having A = absent, M = marginal, or P = present detection calls at all examined time points (T0 – T6, in hours). A. niger conidia developed over time and extracted RNA was used to probe the GeneChips.

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Additional file 2:

Differentially expressed genes at T0-T6. Fold-changes of transcript levels from GeneChips between examined time points (T0-T1, T1-T2, T2-T4, T4-T6) as generated by GeneSpring using CEL.files as inputs, and groupings into KEGG categories.

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Additional file 3:

Expression values and KEGG analysis of differentially expressed genes. Single and combined mapping scores and RPKM values for all genes in dormant (T0) and germinating (T1) conidia, statistical significance values calculated using R package DEGseq [52] and, categorization according to the KEGG database.

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Additional file 4:

GO analysis of differentially expressed genes. Gene ontology categories in up-regulated and down-regulated groups of genes (FetGOat: http://www.broadinstitute.org/fetgoat/index.html webcite) using RNA-seq data.

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Additional file 5:

Differentially expressed genes at T0-T1. Fold-changes of transcript levels from RNA-seq and GeneChips compared side by side.

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Additional file 6:

Antisense and sense transcription profiles. Antisense and sense RPKM values and their ratios in dormant (T0) and germinating (T1) conidia for all the genes with detected AS transcription at any time generated by Ht-seq.

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Additional file 7:

Primers used in this study. Primers and their sequences used for strand-specific cDNA synthesis, RT-PCRs and strand-specific RT-PCRs.

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