biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsGillian McHugotranscription profiling by arrayBos taurusBos taurushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14517Affymetrix® Bovine Genome Array data sets generated for 40 peripheral blood mononuclear cell (PBMC) samples from 10 African cattle (5 trypanotolerant N’Dama and 5 trypanosusceptible Boran) collected at four time points (before infection and at 14, 25, and 34 days post infection) for a Trypanosoma congolense infection experiment.biostudies-arrayexpressSample Collection - Peripheral blood (200 ml) was collected in heparinised syringes before infection and at 14, 25, and 34 days post infection. Peripheral blood mononuclear cell (PBMC) samples were isolated from the blood samples with Percoll™ gradients (GE Healthcare, Buckinghamshire, UK).Growth Protocol - The cattle, all female and aged between 19–28 months, were reared together at the International Livestock Research Institute (ILRI) ranch at Kapiti Plains Estate, Kenya which is located in an area free from tsetse flies and trypanosomiasis (O'Gorman et al. 2006).Sample Treatment - The cattle were experimentally infected with the Trypanosoma congolense clone IL1180 (Geigy & Kauffmann 1973; Nantulya et al. 1984) delivered via the bites of eight infected tsetse flies (Glossina morsitans morsitans) (Akol & Murray 1982; Dwinger et al. 1987) at the ILRI laboratories in Nairobi, Kenya. The flies were allowed to feed on the shaved flanks of the animals until engorgement. The infections were carried out in three batches which took place two weeks apart and were confirmed by microscopy. Parasitaemia and anaemia measured by packed cell volume (PCV) were monitored throughout the course of the infection (O'Gorman et al. 2006).Nucleic Acid Extraction - Total RNA was extracted from the PBMCs in TriReagent (Molecular Research Center, Inc., Cincinnati, OH, USA) and the RNA samples were then DNase-treated and purified using an RNeasy mini kit (Qiagen Ltd., Crawley, UK). RNA quality and quantity was assessed using the 18S/28S ratio and RNA integrity number (RIN) on an Agilent Bioanalyzer with the RNA 6000 Nano LabChip® kit (Agilent Technologies, Inc., Santa Clara, CA, USA).Labeling - cDNA labelling was performed by Almac Diagnostic Services (Craigavon, Northern Ireland) using a one-cycle amplification/labelling protocol.Hybridization - Hybridisation was performed by Almac Diagnostic Services (Craigavon, Northern Ireland).Scaning - Scanning was performed by Almac Diagnostic Services (Craigavon, Northern Ireland). Gene expression data in the form of cell intensity files (.CEL) were generated using the Affymetrix GeneChip® Operating Software (GCOS) package.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsJohn BrowneKieran MeadeDavid MacHughGillian McHugoEmmeline HillGrace O'GormanThomas HallJames WardData Transformation - Quality control with log transformation was performed using affy (v. 1.80.0) (Gautier et al. 2004), Biobase (v. 2.62.0) (Huber et al. 2015), and arrayQualityMetrics (v. 3.58.0) (Kauffmann et al. 2009) with R (v. 4.3.2) (R Core Team 2023). As in previous microarray studies, any individual samples that were identified as outliers in two or more quality control tests were discarded from the analysis (Rue-Albrecht et al. 2014). Normalisation was performed using farms (v. 1.25.0) (Hochreiter et al. 2006) with R (v. 4.3.2). Informative probe sets were identified and extracted using farms (v. 1.25.0) with R (v. 4.3.2).falseTranscription profiling time series of PBMC from two cattle breeds infected with Trypanosoma congolenseAffymetrix® Bovine Genome Array data sets generated for 40 peripheral blood mononuclear cell (PBMC) samples from 10 African cattle (5 trypanotolerant N’Dama and 5 trypanosusceptible Boran) collected at four time points (before infection and at 14, 25, and 34 days post infection) for a Trypanosoma congolense infection experiment.2025-07-17T00:00:00Z2025-07-16T20:00:41.932Z2024-10-07T20:13:24.527ZE-MTAB-14517E-MEXP-1778EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003816EFO_0003969EFO_0003815