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E-GEOD-24086 - Alterations in the Brain Transcriptome in Plasmodium Berghei ANKA Infected Mice

Status
Released on 16 September 2010, last updated on 2 May 2014
Organism
Mus musculus
Samples (12)
Array (1)
Protocols (10)
Description
We have used cDNA microarrays to compare gene expression profiles in brains from normal mice to those infected with the Anka strain of Plasmodium berghei, a model of cerebral malaria. For each of three brains in each group, we computed ratios of all quantifiable genes with a composite reference sample and then computed ratios of gene expression in infected brains with untreated controls. Of the almost 12,000 unigenes adequateluy quantified in all arrays, about 3% were significantly downregulated (p<0.05, >50% fold change) and about 7% were upregulated. Upon inspection of the lists of regulated genes, we identified a high number encoding proteins of importance to normal brain function or associated with neuropathology. These results emphasize the important impact of malarial infection on gene expression in brain and provide tentative target biomarkers that might provide novel therapeutic targets for neurological sequelae of disease. We have used a previously published protocol (Iacobas et al., Physiol Genomics 2005) and a composite reference RNA sample (R) prepared in sufficient quantity for the entire experiment from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females). This combination of source tissues provided a high diversity of genes expressed in the midrange of the detection system for the AECOM mouse cDNA microarrays. Briefly, 60μg total RNA, extracted in Trizol® (Invitrogen, Carlsbad, CA) from brains of three infected (I) and three control (C) mice, purified with RNeasy® mini kit (Qiagen, Valencia, CA), were reverse transcribed into cDNA incorporating fluorescent Cy3-dUTP. The composite reference was reverse transcribed to incorporate Cy5-dUTP. Each of the six Cy3-labeled brain extracts was co-hybridized overnight at 50°C against the Cy5-labeled reference with AECOM 32k Mouse oligonucleotide arrays, MO3 printing series (platform described in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL5371). After hybridization, the slides were washed at room temperature, using solutions containing 0.1% sodium dodecyl sulfate (SDS) and 1% SSC (3M NaCl + 0.3M sodium citrate) to remove the non-hybridized cDNAs.
Experiment type
transcription profiling by array 
Contacts
Dumitru Andrei Iacobas <dumitru.iacobas@einstein.yu.edu>, David C Spray, Dumitru A Iacobas, Herbert B Taniwitz, Louis M Weiss, Mahalia Desruisseaux, Sanda Iacobas, Shankar Mukherjee
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-24086.idf.txt
Sample and data relationshipE-GEOD-24086.sdrf.txt
Processed data (1)E-GEOD-24086.processed.1.zip
Array designA-GEOD-5371.adf.txt
Links