Comparison of undifferentiated ES cell lines HM1, IMT11, SHBL6.3. Mus musculus

3 different ES cell lines were compared in order to determine whether there are significant expression profile differences between ES cell lines, or whether the constraints of maintaining pluripotency in culture force a similar expression profile on cell lines derived from disparate sources. Our results indicate that the latter is more likely. We identified 21 genes that were significantly differentially regulated, either on comparison with the pooled control, or on direct comparison of individual ES cell line data from different slides. Using semi-quantitative RT-PCR on 3 separate isolates from each cell line, we have confirmed 4 of these genes as consistently differentially regulated, Hprt, and 3 others. We would conclude therefore that different ES cell lines at the same passage number in identical culture conditions show very similar expression profiles. Keywords: cell type comparison Overall design: Cardiff University Array Facility NIA 15K slides were used in conjunction with 3 different RNA isolates from each of the ES cell lines. A pooled control was assembled using equal quantities of cells from each cell line, RNA was extracted and labelled, for use on every slide. Fluor switches were carried out, and 12 replicates were used for each cell line (3 biological replicates). The ES cell lines were each derived from different sources; IMT11 cells are derived from 129 strain mice. HM1 cells are also derived from 129 mice, but are missing a functional copy of Hprt. SHBl6.3 cells are derived from the less permissive C57Bl6/J mouse strain. Data were analysed as described in the GSM submissions.