Open Access Research article

Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei

Sarah Kabani1, Katelyn Fenn1, Alan Ross2, Al Ivens3, Terry K Smith4, Peter Ghazal2 and Keith Matthews1*

Author Affiliations

1 Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, UK

2 Division of Pathway Medicine, University of Edinburgh Medical School, Chancellor's building, University of Edinburgh, Edinburgh, UK

3 Fios Genomics Ltd, ETTC, King's buildings, Edinburgh, UK

4 Centre for Biomolecular Sciences, The North Haugh, St Andrews University, UK

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BMC Genomics 2009, 10:427  doi:10.1186/1471-2164-10-427

Published: 11 September 2009

Additional files

Additional file 1:

Pairwise comparisons between slender and individual time-points for all genes represented on the microarrays. Each column contains data with respect to each oligonucleotide represented on the array, with the parent Gene ID, product description, Protein ID, oligonucleotide sequence, oligonucleotide co-ordinates, signal intensity and statistical association provided for each. Annotations with respect to the presence of a signal peptide, transmembrane domain or GO classification are also detailed.

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Additional file 2:

Pairwise comparisons between different individual time-points for all genes represented on the microarrays. Each column contains data with respect to each oligonucleotide represented on the array, with the parent Gene ID, product description, Protein ID, oligonucleotide sequence, oligonucleotide co-ordinates, signal intensity and statistical association provided for each. Annotations with respect to the presence of a signal peptide, transmembrane domain or GO classification are also detailed.

Format: ZIP Size: 12.5MB Download file

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Additional file 3:

Expression profile of all genes or those 407 genes exhibiting Log2 differential expression (P < 0.001) at one or more time points during differentiation. Relative fold change in expression is given relative to stumpy forms (T0). Genes are sorted on the basis of relative differential between slender and stumpy forms, with genes up-regulated in slender forms with respect to stumpy forms having a positive value and genes down-regulated having a negative value. Associated statistical values for each comparison are available in Additional file 1 and Additional file 2.

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Additional file 4:

Genes exhibiting Log2 differential expression (adj P < 0.05 or adj P < 0.1) between pleomorphic slender and stumpy forms. Sheet 1 shows genes up-regulated in slender forms with respect to stumpy forms; sheet 2 shows genes up-regulated in stumpy forms with respect to procyclic forms.

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Additional file 5:

Genes elevated in stumpy forms versus all other samples (trinary code profile -1,-1,-1,-1,-1) and genes elevated in stumpy cells and cells at T1 (i.e. 1 hour into the differentiation programme) (trinary code profile 0,-1,-1,-1,-1). Analysis of stumpy-enriched transcripts; only genes significant at the p < 0.05 level in one or more comparisons are considered, with the Log2 differential for each gene in each of the comparisons being assigned a trinary code based on whether the value was <-1 (code= -1), >1 (code= 1), or -1>x>1 (code= 0). Values are expressed relative to the expression of each gene in stumpy forms (T0) and are in the order T1 vs. T0, T6 vs. T0; T18 vs. T0; T48 vs. T0 and SL vs. T0.

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Additional file 6:

Summary of transient expression changes during differentiation to procyclic forms. Genes were assigned to each temporal group based on their inclusion in the trinary profiles of transiently regulated genes.

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Additional file 7:

Expression profiles of genes exhibiting transient expression during differentiation. Individual profiles of different transiently expressed groups as assigned to distinct trinary codes during the differentiation programme.

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Additional file 8:

Gene ontology analysis for genes temporally regulated during differentiation. Genes on the array have been assigned annotation from any or all of the three gene ontologies (Biological process, BP; Molecular function, MF; cellular compartment, CC). The charts show the representation within distinct Gene ontology groups of significant genes (P < 0.05) within each comparison. Genes up-regulated and down-regulated are shown separately.

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Additional file 9:

Chromosomal location of the genes encoding regulated transcripts. Physical clustering of genes exhibiting differential expression (P < 0.05) in the comparisons T1 vs. T0; T6 vs. T0; T18 vs. T0; T48 vs. T0 and SL vs. T0. The trinary codes for each gene significant at the 5% level were plotted in physical order along each chromosome. Blue denotes down-regulation, Red denotes up-regulation, white indicates 'no change'. No evidence of clustering was observed.

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