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Project microarray data

Raw data is available from Array Express. The files on this page contain the normalised data from each chip for each experiment that was used in our analyses. Sets are available as plain text or MAXD native format for direct import into the MAXD microarray analysis package

Cow Time Course

We have use microarrays to follow the effect of infection on Boran and N'Dama for five weeks post infection and the main results have been published in Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection

Twenty-five susceptible (Boran) and 25 trypanotolerant (N'Dama) cattle were selected from the herd at the ILRI Kapiti plains ranch, which is free from tsetse flies and trypanosomiasis. Cattle were infected by tsetse-mediated inoculation of trypanosomes. Each individual was exposed to 8 flies infected with T. congolense IL1180. Parasite detection and quantification was performed by microscopic examination of the peripheral blood using the dark-ground-buffy coat method. Anaemia was assessed by microhaematocrit.

Twenty-five animals of each breed were included in the expression analysis experiment. Prior to infection, five animals of each breed were killed for collection of control tissue samples, and needle liver biopsies were taken from the remainder. Five animals of each breed were killed on days 21 and 35 p.i. for collection of liver, spleen and precrural lymph node samples. Needle liver biopsies were taken from five animals of each breed at six additional time points (days 12, 15, 18, 26, 29 and 32 p.i.) ensuring a minimum of 14 days between biopsies for any given animal.

Total RNA was extracted from tissues pulverised under liquid nitrogen using the Trizol method (GIBCO BRL). Total RNA was treated with DNAseI and purified with RNAeasy (Qiagen). RNA quality was assessed using an Agilent bioanalyser 2000 (Agilent technologies) and only those samples with RIN > 6.3 were used for downstream procedures.

Expression data was acquired on Affymetrix Bovine Genome arrays, which have probesets for 23,000 transcripts. Samples were randomised before hybridisation such that samples from the different challenge batches were not all hybridised together. 5μg of total RNA preparation was labeled using the One-Cycle Eukaryotic Target labeling protocol (Affymetrix) and labeled targets were hybridized to Bovine Genome array chips. Data were acquired from the hybridized chips with an Affymetrix Gene Chip 3000 scanner. Any sample that failed the labeling or hybridization data quality control using dChip or principal component analysis using SVD in the MAXD package was discarded and the procedure repeated on a new RNA preparation from the original tissue sample. A total of 160 RNA samples passed the quality criteria and the data was normalized using RMA (Robust Multichip Average). Additionally, sets of 25mer probes for each gene represented on the array were identified using AffyProbeMiner and normalisation was carried out in the R environment using multi-mgmos. Raw data for each chip is available from array express E-MEXP-1778.

These files can be viewed and analysed in the open source MaxD environment. Text files are available on request from harry at liv.ac.uk

Mouse Time Course

Spleen, liver and kidney samples were collected from 25 mice at days 0, 3, 7, 9 and 17 post infection with T. congolense strain IL1180. Pools of RNA from five mice are hybridised to five Affymetrix 420 2.0 Mouse expression arrays for each condition, except for kidney for which only times 0 and 7 were hybridised. Full details are included in the papers using the data listed below. Raw data is available from Array Express under accession number E-MEXP-1190.

Publications that have used this data

2010

PDF OF PAPER

A Comprehensive Genetic Analysis of Candidate Genes Regulating Response to Trypanosoma congolense Infection in Mice Ian Goodhead, Alan Archibald, Peris Amwayi, Andy Brass, John Gibson, Neil Hall, Margaret A. Hughes, Moses Limo, Fuad Iraqi, Stephen J. Kemp, Harry A. Noyes PLoS Neglected Tropical Diseases 2010 4(11): e880. doi:10.1371/journal.pntd.0000880

2011

PDF OF PAPER

Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection Harry Noyes, Andy Brass, Isaiah Obara, Susan Anderson, Alan L. Archibald, Dan G. Bradley, Paul Fisher, Abigail Freeman, John Gibson, Michael Gicheru, Laurence Hall, Olivier Hanotte, Helen Hulme, Declan McKeever, Caitriona Murray, Sung Jung Oh, Catriona Tate, Ken Smith, Miika Tapio, John Wambugu, Diana J. Williams, Morris Agaba, and Stephen J. Kemp Proceedings of the National Academy of Sciences 2011 31;108(22):9304-9. doi: 10.1073/pnas.1013486108

2009

PDF OF PAPER

Mechanisms controlling anaemia in Trypanosoma congolense infected mice. Noyes H., Alimohammadian M., Agaba M., Brass A., Fuchs H., Gailus-Durner V., Hulme H., Iraqi F., Kemp S., Rathkolb B., Wolf E., de Angelis M., Roshandel D., Naessens J. PLoS One. 2009 44:e5170

2007

pdf image and link Systematic Strategy for Large-Scale Analysis of Genotype-Phenotype Correlations: Identification of candidate genes involved in African Trypanosomiasis. Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp SJ, Stevens R & Brass A. Nucleic Acids Research 2007 35 5625-5633.