One and four month formalin-fixed paraffin embedded biopsies from 48 kidney transplant recipients (24 AKI donors, 24 non-AKI) underwent global gene expression profiling using DNA microarrays (96 arrays). At one month, there were 898 differentially expressed genes in the AKI group (p-value <0.005; FDR <10%), but by 4-months there were no longer any differences.
Overall design
One and four month formalin-fixed paraffin embedded (FFPE) biopsies from 48 kidney transplant recipients (24 AKI donors, 24 controls; 96 total samples) were profiled using Affymetrix U133PM Plus PM plate arrays on a GeneTitan MC instrument. All samples were selected from the SCD cohort only. AKI donor and controls samples were matched by date of transplantation. Total RNA was extracted from four 20-micron sections using Ambion RecoverAll Total Nucleic Acid Kit and processed for chip hybridization using the new Affymetrix SensationPlus™ FFPE Amplification and 3’ IVT Labeling kit according to the manufacturer’s protocol. Quantile data normalization by RMA and analysis was performed using Partek Genomics Suite for PDR-corrected differential gene expression by ANOVA. Pathway mapping was performed using Ingenuity Pathway Analysis (IPA).
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