alysis parameters. The raw data were also analyzed by GeneSpring GX software version 7. 3. 1. The correlation coefficients of gene probes expressed between any two samples were cal culated from the normalized values by using GeneChip Robust Multiarray Average algorithm. It may be noted that Affymetrix GeneChip expression analysis can be used as a stand alone quantitative comparison, since the correlation between Affymetrix GeneChip results and TagMan RT qPCR results was shown in a good line arity of R2 0. 95 by the MicroArray Quality Control Study, a collaborative effort of 137 scientists led by the US FDA. A hierarchical clustering and principle component analysis of the eight Affymetrix Gene Chip data from duplicates of four populations of hES cells were also performed in order to check the quality of microarray results.

Analyses of signaling pathways and GO process networks The abundantly expressed mRNAs of T3 HDF and T3 CMHD, as well as T3 MEF and T3 CMMEF, cells were analyzed for signal ing pathways and GO process networks by using Meta Core Analytical Suite as previously described. The MetaCore includes Batimastat a curated database of human protein interaction and meta bolism, and thus it is useful for analyzing a cluster of genes in the context of regulatory network and signaling pathways. Quantification of miRNAs The expression levels of 365 human miRNAs from T3 HDF and T3 CMHD cells were determined using the TaqMan MicroRNA Assays. The detailed procedure for miRNA quanti fication was previously described. In brief, TagMan MicroRNA Assays include two steps, stem loop RT fol lowed by real time PCR.

Each 10 ul RT reaction that includes 90 ng total RNA, 50 nM stem loop RT primers, 1�� RT buffer, 1. 25 mM each of dNTPs, 0. 25 U ul RNase inhibitor, and 10 U ul MultiScribe Reverse Transcriptase was incu bated in the PTC 225 Peltier Thermal Cycler for 30 min each at 16 C and at 42 C, followed by 5 min at 85 C, and then held at 4 C. RT products were diluted twenty times with H2O prior to setting up PCR reaction. Real time PCR for each miRNA was carried out in triplicates, and each 10 ul reaction mixture included 2 ul of diluted RT product, 5 ul of 2�� TagMan Universal PCR Master Mix and 0. 2 uM TagMan probe, respectively. The reac tion was incubated in an Applied Biosystems 7900HT Sequence Detection System at 95 C for 10 min, followed by 40 cycles of 95 C for 15 sec and 60 C for 1 min.

The threshold cycle is defined as the fraction cycle num ber at which the fluorescence exceeds the fixed thresh old of 0. 2. Total RNA input was normalized based on the Ct values of the TagMan U6 snRNA assay as an endogenous control. The fold change was calculated as 2 CT �� K, where CT ? and K is a constant. 2D gel analysis of proteins Approximately 1 �� 106 hES cells on 10 cm plate were washed twice each with 1�� PBS and cell wash buffer, and then lyzed using NP40 lysis buffer. 1 mL ice cold acetone 11% w v trichloroacetic acid 20 mM DTT was added per 0. 1 mL solubilised sample