he differentially altered pathways of unique genes, the top three pathways in T3 scientific assay HDF cells are cell adhesion, Inhibitors,Modulators,Libraries immune response and signaling transduction. The top three pathways in T3 CMHDF cells are development, cytos keleton remodeling and immune response. The top three pathways in T3 MEF cells are cell adhesion, cytoskeleton remodeling and regulation of metabolism. The top two pathways in T3 CMMEF cells are cytoskeleton remodeling and cell Inhibitors,Modulators,Libraries adhe sion. Expression profiling of miRNAs The expression profiles of 365 human miRNAs in T3 HDF and T3 CMHDF cells were quantitated using TaqMan miRNA Assays as described previously, and the expression level of each miRNA was indicated as folds over U6 snRNA. The average values of triplicate analyses and fold changes for 365 miRNAs from these two different cell populations are given in Additional file 7, Table S3.

The Pearson correlation coefficient of r 0. 9198 between T3 HDF and T3 CMHDF cells indicates their similar miRNA expression profiles. The expression levels and fold changes of 35 most abundantly expressed miRNAs of T3 HDF and T3 CMHDF, as well as those Inhibitors,Modulators,Libraries of 31 miRNAs of T3 MEF and T3 CMMEF, cells are summarized in Table 2. These results indicate that nine hES cell spe cific miRNAs were abundantly expressed in T3 HDF and T3 CMHDF cells, and that miR 367 and miR 373 had little more than 2 fold variations between these two cell populations. In addition, eleven other miRNAs appeared to express more than 2 folds in T3 CMHDF compared with T3 HDF cells.

It may also be noted that the miRNA data of T3 MEF and T3 CMMEF cells were previously determined using the set of 250 miRNAs Inhibitors,Modulators,Libraries in which miR 302a, 302b, 302c and 373 were not included, and that very similar expression profiles of miRNAs between T3 MEF and T3 CMMEF cells were also found pre viously. No miRNA with more than 2 fold variation was found between the 31 abundantly expressed miR NAs of T3 MEF and T3 CMMEF cells. Protein patterns of 2D gel analysis The total soluble proteins extracted from T3 HDF and T3 CMHDF, Entinostat as well as T3 MEF and T3 CMMEF, cells were separated on 2D gels, and the silver staining pat terns of protein spots from these four hES cell popula tions appeared to be very similar. The similarities of protein spot patterns among these four 2D gels were analyzed using ImageMaster, and their results are indicated in Table 3.

A total of approximately 1627 spots were separately detected, and approximately 1161 spots were matched among these four cell populations. It may be noted that the ranking orders of similarities among these four com parisons of protein spots were found to be the same to those of correlation coefficients of mRNAs and that the correlation coefficient between sellectchem % protein match spots and correlation coefficient of mRNAs was found to be 0. 8122. In other words, the similarities of protein expression among these four cell populations were con sistent with those of mRNA expression, although the extents of their protein similarities were