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Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon

Giselda Bucca1, Emma Laing1, Vassilis Mersinias13, Nicholas Allenby1, Douglas Hurd2, Jolyon Holdstock2, Volker Brenner2, Marcus Harrison2 and Colin P Smith1*

Author Affiliations

1 Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK

2 Oxford Gene Technology Ltd, Begbroke Business Park, Sandy Lane, Yarnton, Oxford OX5 1PF, UK

3 Current address: Institute of Immunology, Biomedical Sciences Research Centre "Alexander Fleming", Athens 16672, Greece

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Genome Biology 2009, 10:R5  doi:10.1186/gb-2009-10-1-r5

Published: 16 January 2009

Additional files

Additional data file 1:

Average (across biological replicates) plotted as [log2 Antibody bound/Total chromatin - log2 'No Antibody' bound/Total chromatin]. The red line indicates the threshold applied to identify enriched probes.

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Open Data

Additional data file 2:

Average (across biological replicates) plotted as [log2 Antibody bound/'No Antibody' bound]. The red line indicates the threshold applied to identify enriched probes.

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Open Data

Additional data file 3:

The anti-HspR-enriched probes are plotted on a linear scale. Open circles indicate the start co-ordinate (relative to genome sequence) of each probe that passed quality control filtering. The genetic organization of each region is indicated below the plot; each arrow represents a coding sequence or stable RNA gene as defined in [EMBL:AL645882.2].

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Open Data

Additional data file 4:

Tabulation of genes significantly up-regulated following heat-shock at 42°C.

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Open Data

Additional data file 5:

Tabulation of genes significantly up-regulated in an hspR disruption mutant relative to wild-type.

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Open Data

Additional data file 6:

Partial matches to the HspR-binding consensus sequence within the five tRNAGln/Glu cluster.

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Open Data

Additional data file 7:

Motif identified from MEME analysis of the HspR targets identified with the Sco-Chip2-v2 array.

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Additional data file 8:

Over-representation of amino acids in heat-shock induced gene products (listed in Additional data file 4) relative to all annotated proteins from the S. coelicolor genome [EMBL: AL645882.2].

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Open Data

Additional data file 9:

SCO3202 (hrdD) and SCO4157 had respective rank products pfp values of 0.12 and 0.13. SCO4410 and SCO5639 were identified as new putative targets for HspR. Average values are plotted from the same two independent biological replicates of each condition used in the array-based expression analysis.

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Open Data

Additional data file 10:

Average values are plotted from the same two independent biological replicates of each condition used in the array-based expression analysis.

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Open Data

Additional data file 11:

Comparison of expression of heat-shock genes from SMMS surface-grown cultures (Additional data file 4) in YEME+10.3% sucrose liquid cultures (as used in ChIP-on-chip experiments).

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Open Data

Additional data file 12:

Probes found to be significantly enriched for HspR on Sco-Chip2-v1 arrays.

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Open Data

Additional data file 13:

Probes found to be significantly enriched for HspR on Sco-Chip2-v2 arrays.

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Open Data

Additional data file 14:

An enlarged image of Figure 3d (rrnD data), with a dotted line along log ratio of 0.

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Open Data

Additional data file 15:

An enlarged image of Figure 3e (tRNA cluster data), with a dotted line along log ratio of 0.

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Open Data