The mouse and human CEL files were processed using the GenePattern analysis pipeline (www.genepattern.com ). CEL file normalization was performed with the Robust Multichip Average (RMA) method using the mouse and human Entrez-Gene custom CDF annotation from Brain Array version 10 http://brainarray.mbni.med.umich.edu/Brainarray/default.asp ). The normalized files were log2 transformed and batch correction was performed for the NZB/W and NZW/BXSB murine data (25 (link)).
The poly-A RNA control kit was used in processing the mouse microarray data. The expression baseline was defined by calculating the gene expression median of each gene, and adding one standard deviation to the minimum value obtained. Of the 16539 mouse genes represented on the Affymetrix genechip, 13425, 13600 and 14252 were expressed above the defined expression baseline in NZB/W, NZM2410 and NZW/BXSB respectively. Of the 12029 human genes, 11285 and 11429 were expressed above the 27 Poly-A Affymetrix control expression baseline (negative controls) in the glomerular and tubulointerstitial compartments respectively and were used for further analyses. Mouse and human normalized data files are uploaded on Gene Omnibus website (http://www.ncbi.nlm.nih.gov/geo/ ) and accessible under reference numbers [GEO: GSE32583 and GSE32591].
IgA nephropathy (IgAN) and hypertensive nephropathy (HT) gene expression profiles from ERCB cohorts were available to the investigators as part of an independent study (Wenjun Ju et al, manuscript under review) and were compared with the presented LN data. IgAN and HT data are available on GEO under the reference number GSE35488 and GSE37463 (the last one will be activated after acceptance of the manuscript).
The poly-A RNA control kit was used in processing the mouse microarray data. The expression baseline was defined by calculating the gene expression median of each gene, and adding one standard deviation to the minimum value obtained. Of the 16539 mouse genes represented on the Affymetrix genechip, 13425, 13600 and 14252 were expressed above the defined expression baseline in NZB/W, NZM2410 and NZW/BXSB respectively. Of the 12029 human genes, 11285 and 11429 were expressed above the 27 Poly-A Affymetrix control expression baseline (negative controls) in the glomerular and tubulointerstitial compartments respectively and were used for further analyses. Mouse and human normalized data files are uploaded on Gene Omnibus website (
IgA nephropathy (IgAN) and hypertensive nephropathy (HT) gene expression profiles from ERCB cohorts were available to the investigators as part of an independent study (Wenjun Ju et al, manuscript under review) and were compared with the presented LN data. IgAN and HT data are available on GEO under the reference number GSE35488 and GSE37463 (the last one will be activated after acceptance of the manuscript).
