User:Matthew Whiteside/Notebook/Malaria Microarray/2009/09/09

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Mouse Malaria Microarray Datasets

  • A meta-analysis will combine results from multiple studies to increase statistical confidence in results. End result is a Gene-Level Expression Matrix containing z-values or some similar measure of effect size across the different studies. This matrix will then be used in downstream system biology analysis.
  • Step one in the meta-analysis of mouse malaria microarray datasets is selection of datasets with similar experimental conditions.
  • Outlined below are all mouse malaria studies that have publicly available microarray data (in GEO or ArrayExpress). I've also listed the relevant information that will guide the selection of studies for the meta-analysis:

Potential Studies

ID Authors PMID Malaria Strains Mouse Strains RNA Source Tissues Infection route Platform Timepoints Replicates Research Objectives Normalized Data Available
GSE5672 Lovegrove et al. (Hughes Lab) 17118208 PbA CB57BL/6 (susceptible), BALB/c (resistant) Brain, Liver, Lung, Spleen No details GPL4220 - custom mouse & malaria oligo array Day 0,3,6 None Simultaneous profiling of host and pathogen response in CM infection, comparing susceptible & resistant strains. Not thru GEO
GSE7814 Lovegrove et al. (Hughes Lab) 17991715 PbA C57BL/6 (susceptible), BALB/c (resistant) Brain No details GPL8321 Affy Mouse Genome 430A 2.0 Day 0,1,3,6 2 tech reps, 2 bio reps Compare susceptible mouse strain to non-susceptible Not thru GEO
GSE6019 Randall et al. 18474652 PbA C57BL/6 (susceptible) & CBA/CaH (susceptible) Brain 10e5 infected RBCs GPL1261 Affy Mouse Genome Array 430 2.0 Onset of CM symptoms (day 6 or 7) pooled RNA from 6 mice Compare 2 susceptible strains to see if similar pathways involved Not thru GEO
GSE9808 Miu et al. 18299338 PbA (CM-strain), PbK (Non-CM strain) C57BL/6 Brain No details PGL1261 Affy Mouse Genome Array 430 2.0 (1st rep) PGL1832 Mouse Compugen 22k array (subsequent reps) Day 6 (PbA), Day 6,14 (PbK) 5 bio reps Compare pathways of CM and Non-CM infection - both fatal No thru GEO
GSE9497 Lovegrove et al. (Hughes Lab) 18483551 PbA C57BL/6 Lung No details PGL4220 Custom UTTH_Mouse/P.bergheiANKA 44k oligo array Day 6 5 mice pooled with tech reps (dye-swaps) Lung infection, role of CD36 (see paper, further experimentation performed) No thru GEO