DNA and expression analysis of transchromosomic cell lines and mice carrying Hsa21. (A) Hsa21 content in five transchromosomic ES cell lines (74-2c1, 80-2, 80-6c2, 86-1, and 91-1) and Tc1 mouse DNAs. Cell line and mouse names are shown above the vertical bars that indicate the presence of the Hsa21 markers listed on the left. Markers are shown in order but are not spaced relative to their distance apart on Hsa21 (positions are given in table S1). Red denotes the presence of the marker, gray denotes not scored, and a blank space denotes a negative score, i.e., the marker was not present. CXADR was shown to be present by microarray results from Tc1 embryos. The vertical black line on the right is a scaled representation of the physical map of Hsa21, showing the relative spacing and maximum sizes of the two gaps. cen, centromere. (B to E) RNA samples from two Tc1 whole embryos and one wild-type littermate (E14.5) were hybridized to Affymetrix HG-U133A GeneChips. Array data were scaled to a target intensity of 500 before analysis. (B and C) Scatter plots showing Hsa21 gene signal intensities of embryos (B) Tc1-a and (C) Tc1-b against the wild-type littermate. (D) Scatter plot showing Hsa21 gene signal intensities of embryo Tc1-a against Tc1-b as a hybridization control. In each scatter plot, red points represent genes called present in both embryos, orange points represent genes called present in one of the two embryos, and gray points represent genes below the threshold for detection in both embryos. Diagonal lines indicate the thresholds for twofold, threefold, tenfold, and thirtyfold differences between the two embryos. (E) Genes with increased expression in Tc1 embryos compared to wild-type embryos. Red lettering indicates those found with the reduced stringency search method. Underlined genes were also found by RT-PCR or immunoblot. Expression of one gene, SIM2 (green), was detected by RT-PCR but not by microarray analysis.