The protective HLA group includes all individuals with at least one protective HLA allele

that human-specific miRNAs are enriched in the highly expressed miRNAs in hES/hiPS-g. In contrast, when we listed miRNAs that have higher expression levels in hSomatic-g than in hES/hiPS-g, the list included only 12060783 two primate-specific miRNAs. Members of the let-7 group, which are involved in developmental timing and expressed at higher levels in fibroblasts than in ESCs, are on the list, in accordance with a previous study. Analysis of Human miRNA Profiles We next performed clustering analysis of miRNA expression patterns. Before the analysis, we excluded the 118 miRNAs with Ct values greater than 30 in all samples. The remaining 263 miRNAs were subjected to HC and NMF according to DCt values. Both analyses showed clear segregation of ES/iPS cells from other cells. EBs were located closer to the ES/iPS cell cluster. In the somatic cells, two peripheral blood mononuclear cells and two dermal fibroblast cells were closely clustered. In the ES and iPS cell lines, three human ES cell lines were closely clustered, but clustering did not reflect differential clustering with categories of cell origin, methods, or use of ROCK inhibitor. We were interested whether iPS cells have some degree of similarity in miRNA expression pattern based on their origin; however using subsets of samples and/or miRNAs indicated no such relationship, suggesting that reprograming wipes out the characteristics of the original cells, at least in terms of miRNA expression patterns. We then used PCA. The first TG100 115 chemical information component showed clear segregation of ES/iPS and other cells. The second and third components segregated dermal fibroblasts and PBMCs. We then listed the first component eigenvectors. Eigenvectors with absolute values greater than 2 are shown in Analysis of Mouse miRNA Profiles miRNA mmu-miR-290-3p mmu-miR-291a-3p mmu-miR-291b-5p mmu-miR-292-3p mmu-miR-293 mmu-miR-294 mmu-miR-295 mmu-miR-302a mmu-miR-302b mmu-miR-302c mmu-miR-302d mmu-miR-367 mmu-miR-133b mmu-miR-200a mmu-miR-23a mmu-miR-743b-5p doi:10.1371/journal.pone.0073532.t003 Profiling of miRNA in Human and Mouse ES/iPS Cells much higher expression in 17053790 ES/iPS cells than in MEF/TTF. In contrast, miR-743-5p showed no difference, probably because this miRNA had an extremely low value in TTF. All other samples showed similar DCt values. Identification of miRNAs Distinguishing ES and iPS Cells ES and iPS cells are distinguished by gene expression signatures, and we next questioned whether miRNAs exist that can distinguish human ES and iPS cells. We conducted HC and NMF analyses using DCt values for ES and iPS cells under several different sets of conditions, but HC or NMF did not separate ES and iPS cells. Moreover, PCA did not identify miRNAs that clearly distinguish human ES and iPS cells. Profiling of miRNA in Human and Mouse ES/iPS Cells 11 Profiling of miRNA in Human and Mouse ES/iPS Cells values for miR-886-5p are identical in iPSCs and ESCs. Study by Chi et al. listed 16 miRNAs that are differentially expressed in human ES and iPS cells, but only three of them showed similar trends in our study. Chin et al. used oligo DNA-based arrays, and we cannot deny that different miRNA analysis protocols gave different results. Comparison of mouse ES and iPS cells identified several miRNAs that are expressed at significantly different levels in ES and iPS cells, and members of the let-7 and miR-30 families are more highly expressed in iPSCs than in ESCs. targeting Tgfr2 and p21 during the mesenchymal-to-epithelial tr