Fig. 1

Data analysis overview. Stage 1: SLE-iPSCs and NC-iPSCs were used for the extraction of protein and RNA. Stage 2: Proteins were identified with iTRAQ-coupled LC–MS/MS; the libraries of mRNA and miRNA were constructed by using the Illumina TruSeq RNA Sample Prep Kit v2-Set A and TruSeq Small RNA Sample Prep Kit Set A, respectively, and then sequenced by using the Illumina HiSeq™ 2000 System. Stage 3: Protein dates were submitted to the ProteinPilot analysis software for peptide identification and quantification, subsequently, differentially expressed proteins were identified and quantified. Gene expressions based on sequencing were measured by RPKM values, ‘FDR(false discovery rate) ≤0.001 and the absolute value of log2-Ratio ≥1’ as the threshold. Differentially expressed mRNAs and miRNAs were obtained. Stage 4: GO enrichment analysis facilitated the mappings of all differentially expressed proteins, mRNAs and miRNAs to GO terms in the database (http: //www. geneontology.org/). With PicTar, miRanda v5, TargetScan 5.1, differentially expressed target proteins and mRNAs were predicted. Stage 5: Differentially expressed proteins and mRNAs were classified according to the GO database. With Cytoscape software,the regulation network of microRNA-target protein and microRNA-target mRNA were analyzed. Stage 6: An integrated analysis of microRNA, target mRNAs and proteins was carried out using Cytoscape software. Representative miRNA, mRNA and proteins were verified using Q-PCR and western blotting