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We limited our analyses to SNPs that were heterozygous in genomic DNA (from a given individual) and that were consistent with Mendelian inheritance of the parental genotypes. As an additional control, we verified heterozygosity in genomic DNA from each clone. When analyzing cDNA genotypes, we eliminated all SNPs for which we consistently detected only one of the two alleles or for which only one allele was detected in the nonclonal cell line, A further filter was to consider only SNPs that gave a cDNA genotype call for at least two distinct clones
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We limited our analyses to SNPs that were heterozygous in genomic DNA (from a given individual) and that were consistent with Mendelian inheritance of the parental genotypes. As an additional control, we verified heterozygosity in genomic DNA from each clone. When analyzing cDNA genotypes, we eliminated all SNPs for which we consistently detected only one of the two alleles (or for which only one allele was detected in the nonclonal cell line). A further filter was to consider only SNPs that gave a cDNA genotype call for at least two distinct clones.
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Although the data we present are from the 260,000 SNPs present on the Affymetrix Nsp 250 K mapping array, we have also obtained qualitatively similar data from the Sty 250 K mapping array and from the earlier generation 100 K mapping array set
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Although the data we present are from the 260,000 SNPs present on the Affymetrix Nsp 250 K mapping array, we have also obtained qualitatively similar data from the Sty 250 K mapping array and from the earlier generation 100 K mapping array set.
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Several SNPs, particularly at the distal portion of the short arm, showed biallelic expression. The locations of these SNPs fell within areas known to contain genes that escape X-inactivation
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Several SNPs, particularly at the distal portion of the short arm, showed biallelic expression. The locations of these SNPs fell within areas known to contain genes that escape X-inactivation.
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For help with microarray experiments, we thank S. Levy at the Vanderbilt Microarray Shared Resource, V. Morgan at the Harvard Medical School-Partners Healthcare Center for Genetics and Genomics Microarray Facility, and B. Blumenstiel and S. Gabriel at the Broad Institute Center for Genotyping and Analysis. We thank A. Ensminger, M. Tackett, and M. Tipping for help in subcloning cell lines; D. Lucente for help with in vivo experiments; and D. Bartel, A. Bortvin, R. Medzhitov, V. Mootha, P. Sklar, and members of the lab for comments on the manuscript. This work was supported by NIH grants to A.C.
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For help with microarray experiments, we thank S. Levy at the Vanderbilt Microarray Shared Resource, V. Morgan at the Harvard Medical School-Partners Healthcare Center for Genetics and Genomics Microarray Facility, and B. Blumenstiel and S. Gabriel at the Broad Institute Center for Genotyping and Analysis. We thank A. Ensminger, M. Tackett, and M. Tipping for help in subcloning cell lines; D. Lucente for help with in vivo experiments; and D. Bartel, A. Bortvin, R. Medzhitov, V. Mootha, P. Sklar, and members of the lab for comments on the manuscript. This work was supported by NIH grants to A.C.
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