Scanner control software rev 7

Human microRNA microarrays from Agilent Technologies (8*60 K) containing probes for 2549 human microRNAs from the miRBase V21.0 database were used. The microarray image information was converted into spot intensity values using Scanner Control Software Rev. 7.0 (Agilent Technologies, Santa Clara, CA). Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna [27 (link)]. The microarray experiments were performed at Shanghai Biotechnology Corporation and microRNAs with altered expression levels were screened in each experimental group according to the manufacturer’s protocol. The screening cohort included 5 type 2 DM patients, 6 DN patients, and 9 NDRD (4 IgAN and 5 MN) patients.

Human microarrays obtained from Agilent Technologies (Santa Clara, CA, USA) were used in this study. For sample labeling and hybridization, total RNA isolated from HEC-1A cells with transient-silenced RelB versus vehicle control was used as the input. The spot intensity values were converted from microarray image information using Scanner Control Software Rev. 7.0 (Agilent Technologies). For normalization and further analysis, background signal subtraction was performed using GeneSpring GX11.0 software (Agilent Technologies, Santa Clara, CA, USA). Hierarchical clustering was used to group genes from RelB knockdown and controls. KEGG pathway analysis and GSEA were performed to identify gene sets and pathways relevant to gene expression data. GSEA (version 2.2.0) (Cambridge, MA, UK) is a powerful analysis tool for integrating gene expression data with gene sets to identify unified biological themes.^{23 (link)} Significantly differentially expressed genes were verified by qRT-PCR and WB after identification via Z-score fold-change screening.