Computational protocol: The transcription factor Dach1 is essential for podocyte function

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Protocol publication

[…] Human renal biopsy specimens and Affymetrix microarray expression data were procured within the framework of the European Renal cDNA Bank—Kröner‐Fresenius Biopsy Bank., Biopsies were obtained from patients after informed consent and with approval of the local ethics committees. Following renal biopsy, the tissue was transferred to RNase inhibitor and microdissected into glomeruli and tubulointerstitium. Total RNA was isolated from microdissected glomeruli, reverse transcribed and linearly amplified according to a protocol previously reported. The microarray expression data used in this study came from individual patients with DN. Pre‐transplantation kidney biopsies from living donors (LD) were used as control renal tissue. Fragmentation, hybridization, staining and imaging were performed according to the Affymetrix Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA, USA). CEL file normalization was performed with the Robust Multichip Average method using RMAExpress (Version 1.0.5) and the human Entrez‐Gene custom CDF annotation from Brain Array version 18 (http://brainarray.mbni.med.umich.edu/Brainarray/default.asp). To identify differentially expressed genes, the SAM (Significance Analysis of Microarrays) method was applied using TiGR (MeV, Version 4.8.1). A q‐value below .05 was considered to be statistically significant. […]

Pipeline specifications

Software tools RMAExpress, SAM
Application Gene expression microarray analysis
Organisms Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Homo sapiens
Diseases Diabetic Nephropathies, Renal Insufficiency, Chronic