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Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Charissa de Bekker1, Oskar Bruning2, Martijs J Jonker23, Timo M Breit23 and Han AB Wösten1*

Author Affiliations

1 Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Institute of Biomembranes, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands

2 Microarray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands

3 Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28, 6525 GA Nijmegen Nijmegen, the Netherlands

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Genome Biology 2011, 12:R71  doi:10.1186/gb-2011-12-8-r71

Published: 4 August 2011

Additional files

Additional file 1:

A protocol describing the procedure to extract and amplify RNA of single hyphae (or parts thereof).

Format: DOC Size: 47KB Download file

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Additional file 2:

A figure showing the amount of RNA within 1,000 hyphae.

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Additional file 3:

A table, similar to Table 1listing Ct values of a QPCR analysis of the two amplification experiments of RNA from single hyphae (hyphae 1 to 3 and 4 and 5).

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Additional file 4:

A table listing Affymetrix quality control checks after hybridizing amplified cDNA from single hyphal tips.

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Additional file 5:

Scatter plots that show that genes with an absent call in the single hypha analysis are generally lowly expressed in a transcriptome analysis of a population of hyphae from the same zone of the colony.

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Additional file 6:

A table listing the probe sets that gave a present call in at least one of the five arrays of a single hypha.

Format: XLSX Size: 2.2MB Download file

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Additional file 7:

A table listing the overrepresentation of functional gene categories within the probe sets with a present call in each of the individual hyphae.

Format: XLSX Size: 13KB Download file

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Additional file 8:

A table listing the probe sets with a present call in at least one of the five hyphae and a standard deviation > 0.5 between the log2 RMA signals of the single hyphae.

Format: XLSX Size: 279KB Download file

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Additional file 9:

A figure showing P-values of the functional gene categories in Table 4after analyzing hyphae 1 to 5 and hyphae 1 to 3 and 4 and 5 separately.

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Additional file 10:

A table listing the top 100 genes with the highest signal values in each of the five hyphae.

Format: XLSX Size: 80KB Download file

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Additional file 11:

A table listing the genes with the highest signal values that can be found in the top 100 of 2, 3, 4 or 5 out of the 5 single hyphae.

Format: DOC Size: 64KB Download file

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Additional file 12:

A table listing the genes with the highest signal values that can be found in the top 100 of only 1 out of the 5 single hyphae.

Format: DOC Size: 88KB Download file

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