Open Access Highly Accessed Research article

Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling

Paul Lacaze1, Sobia Raza14, Garwin Sing1, David Page1, Thorsten Forster12, Petter Storm1, Marie Craigon1, Tarif Awad3, Peter Ghazal12 and Tom C Freeman14*

Author Affiliations

1 Division of Pathway Medicine, The University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK

2 Centre for Systems Biology at Edinburgh, The University of Edinburgh, Darwin Building, King's Buildings Campus, Mayfield Road, Edinburgh, UK

3 Affymetrix Laboratory, Affymetrix, Inc. 3380 Central Expressway, Santa Clara, USA

4 The Roslin Institute, University of Edinburgh, Midlothian, UK

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BMC Genomics 2009, 10:372  doi:10.1186/1471-2164-10-372

Published: 10 August 2009

Additional files

Additional file 1:

Mock transfection gene expression clusters.

Format: XLS Size: 474KB Download file

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Additional file 2:

Genes differentially regulated in mock transfections (571 genes).

Format: TXT Size: 103KB Download file

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Additional file 3:

Exon-level assessment of gene knockdown by siRNA. Level of knock-down at each of the exon probesets across the entire length of transcripts in the presence of IFNγ. Green profiles represents the median signal intensity in the three control arrays (RISC-Free) and red line the median signal intensity in the three siRNA targeted arrays.

Format: ZIP Size: 1.1MB Download file

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Additional file 4:

Genes differentially regulated by IFNγ (242 genes).

Format: TXT Size: 30KB Download file

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Additional file 5:

Genes differentially regulated by targeting siRNAs in absence of IFNγ (986 genes).

Format: TXT Size: 296KB Download file

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Additional file 6:

Genes differentially regulated by targeting siRNAs in presence of IFNγ (842 genes).

Format: TXT Size: 269KB Download file

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Additional file 7:

Genes differentially regulated by targeting siRNAs in both the absence and presence of IFNγ (456 genes).

Format: TXT Size: 57KB Download file

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Additional file 8:

RNAi gene expression clusters.

Format: XLS Size: 2MB Download file

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Additional File 9:

Macrophage flow cytometry. Mouse bone-marrow derived monocytes were stained on day 6 of differentiation for CD11b and F4/80 cell surface markers to identify the presence of macrophages. Over 99% of cells within the cultures are CD11b and F4/80 positive.

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Additional file 10:

BioLayout3D expression data from mock transfection study.

Format: MHT Size: 234KB Download file

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Additional file 11:

BioLayout3D expression data from targeted RNAi study.

Format: MHT Size: 668KB Download file

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