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. B, g; T5 T n& @7 a貌似是哦，要不帮忙翻译下这几段吧！谢谢 ) z# w+ }- I# \7 I3 S- ~
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We prepared genomic DNA and cDNA from soPS cells and their corresponding somatic cells (Supplementary Fig. 7). By generating 108,982,981 sequencing reads (Supplementary Table 6), we were able to identify 787 and 483 expressed SNPs for soPS1 and soPS2, respectively, for which the oocyte donorDNAsequence differed from that of the somatic cell and for which the somatic cell was homozygous. The median allelic ratio (somatic/(oocyte plus somatic)) for the genomic DNA was 0.64 for both soPS1 and soPS2. This ratio is consistent with the inference that a diploid complement of 46,XY chromosomes originating from the somatic cell and a haploid set of 23,X chromosomes originating from the oocyte are present in the soPS cell lines.3 _9 N" [4 }* A" ~8 O) R& K1 B& ?
To calculate the proportion of transcripts expressed from the somatic cell-derived genome in soPS cells (cDNAsomatic/(cDNAoocyte plus cDNAsomatic)), each individual SNP was normalized to the ratioof the same SNP observed in genomicDNA. If a locus was expressed in proportion to its genomic content in soPS cells, the ratio of transcripts would be expected to equal 2/350.6667. Allele ratios for each SNP were binned in increments of 0.05 units, and thatnumber of transcripts was expressed as a fraction of total SNPs captured (Fig. 4e). (For example, 162 somatic cell SNPs were expressed at a ratio of 0.65–0.7 in soPS1. As the total number of SNPs captured was 787, the fraction is 162/78750.206, yielding the data point indicated by an asterisk in Fig. 4e). The median of the allelic ratio was 0.67 for soPS1 and 0.64 for soPS2, consistent with expression from the somatic genome proportional to the genomic content. The distribution of allelic ratios approximated a Gaussian curve (Shapiro–Wilk test for normalityW50.92 for soPS1 andW50.97 for soPS2), indicating significant variability in the contribution of a particular allele. Such variation was not specific to soPS cells. Variability at comparable levels was also observed for allelic ratios in diploid HUES6 as well as in tetraploid HUES6–somatic cell hybrids31 (Supplementary Fig. 8), and may be caused by polymorphisms in gene regulatory regions30.
4 r3 x: A; v4 A5 |Our expectation was that if reprogramming in soPS cells were incomplete we would detect a bias in this distribution: genes expressed at high levels in fibroblasts, but at low levels in pluripotent stem cells, would be expressed predominantly from the fibroblast cell-derived genome in soPS cells; conversely, genes that are expressed at high levels in pluripotent stem cells, but not in fibroblasts, would be expressed predominantly from the oocyte-derived genome. Amonga total of 1,019 genes represented in both gene expression array as well as in the SNP capture data, 38 (18 for soPS1 and 20 for soPS2) were upregulated at least fourfold in soPS cells (P,0.01), and 69 (45 for soPS1 and 24 for soPS2) genes were expressed in the donor fibroblasts at levels fivefold or higher compared to soPS cells (P,0.01). The mean allelic transcript ratio for the ‘somatic cell genes’ and the ‘pluripotent cell genes’, was identical, and did not differ from the expected allelic ratio of 0.66 nor from the allelic ratio of all captured genes (Fig. 4f and Supplementary Table 7).+ D, b" V6 n2 J. s6 o! x& t
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发表于 2011-12-24 13:46
发表于 2011-12-25 23:52
