Comparison of the transcriptome of hESCs maintained in DC-HAIF or CM. (A) Venn diagram of the distribution of transcripts detected using high-density Illumina Sentrix Human-6 Expression Beadchips containing 47 296 transcript probes in BG02 cells maintained in CM (64 passages) or DC-HAIF (10 or 32 passages in defined medium). A large proportion of the expressed transcripts were detected in all samples. (B) Scatterplot analysis demonstrated that the transcriptional profile of BG02 DC-HAIF p32 cells was highly similar to that of BG02 cells maintained in CM (top panel), and was not substantially altered in early- and late-passage cultures in DC-HAIF (bottom panel). Correlation coefficients (R²) were generated using all detected transcripts with an expression level of more than 0 (black and blue dots), or with transcripts exhibiting a detection confidence level of more than 0.99 (R² select, blue dots). Red lines delineate the mean and limits of a 2-fold difference. (C) Hierarchic clustering dendrogram of relative gene expression in different populations generated using the Beadstudio software (Illumina, San Diego, CA). Early- and late-passage BG02 cells maintained in DC-HAIF clustered tightly (approximately 0.0075) and retained a close similarity to BG02 and BG03 cells maintained in CM (approximately 0.037). Previous analyses showed that different undifferentiated hESC lines clustered tightly (approximately 0.032) compared with differentiated embryoid body populations (approximately 0.0875) or fibroblasts (approximately 0.160).¹⁸