そこに遠藤さんが世界で初めてその区別法を考え付いてネイチャーに提出したが
リジェクトされたんで大隅さんが長をしてる団体の発行している雑誌にその論文を掲載した。
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Quality control method for RNA-seq using single nucleotide polymorphism allele frequency
一塩基多型対立遺伝子頻度を用いたRNA-seqのための品質制御方法
我々は我々の道を行くだけだ。
さて、桂報告と同様の趣旨だがネイチャー掲載の論文では生データが少し出されている。取り敢えず本文だね。
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The STAP stem-cell line GLS1–13 was reported as established from STAP cells prepared from genomic Oct4 fragments (GOF) mice (B6 background) carrying the Oct4-gfp transgene<10> in 2012. All these cell lines have a large truncation with a terminal inverted repeat in one of two X chromosomes (Extended Data Fig. 2a). An identical X chromosome was found in GOF-ES, an ntES cell line established from GOF mice in 2011, but not in parental GOF mice. It is unlikely that such a peculiar X chromosome abnormality would occur independently, strongly suggesting that the GLS lines were derived from the GOF-ES.
<10>Ohbo, K. et al. Identification and characterization of stem cells in prepubertal spermatogenesis in mice. Dev. Biol. 258, 209–225 (2003)
小野小町
GOFマウスってgenomic Oct4 fragmentsの略なのね。2003年にOhbo, K.さんらが自分たちの研究のために開発してたマウスね。こっちの論文のアブストも貼って置いた方がいいのかな。
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Dev Biol. 2003 Jun 1;258(1):209-25.
Identification and characterization of stem cells in prepubertal spermatogenesis in mice.
Ohbo K<1>, Yoshida S, Ohmura M, Ohneda O, Ogawa T, Tsuchiya H, Kuwana T, Kehler J, Abe K, Schöler HR, Suda T.
Author information
<1>The Sakaguchi Laboratory of Developmental Biology, School of Medicine, Keio University, Tokyo 160-8582, Japan. kohbo@sc.itc.keio.jp
Abstract
The stem cell properties of gonocytes and prospermatogonia at prepubertal stages are still largely unknown: it is not clear whether gonocytes and prospermatogonia are a special cell type or similar to adult undifferentiated spermatogonia. To characterize these cells, we have established transgenic mice carrying EGFP (enhanced green fluorescence protein) cDNA under control of an Oct4 18-kb genomic fragment containing the minimal promoter and proximal and distal enhancers; Oct4 is reported to be expressed in undifferentiated spermatogonia at prepubertal stages. Generation of transgenic mice enabled us to purify gonocytes and prospermatogonia from the somatic cells of the testis. Transplantation studies of testicular cells so far have been done with a mixture of germ cells and somatic cells. This is the first report that establishes how to purify germ cells from total testicular cells, enabling evaluation of cell-autonomous repopulating activity of a subpopulation of prospermatogonia. We show that prospermatogonia differ markedly from adult spermatogonia in both the size of the KIT-negative population and cell cycle characteristics. The GFP(+) KIT(-) fraction of prospermatogonia has much higher repopulating activity than does the GFP(+)KIT(+) population in the adult environment. Interestingly, the GFP(+)KIT(+) population still exhibits repopulating activity, unlike adult KIT-positive spermatogonia. We also show that ALCAM, activated leukocyte cell adhesion molecule, is expressed transiently in gonocytes. Sertoli cells and myoid cells also express ALCAM at the same stage, suggesting that ALCAM may contribute to gonocyte-Sertoli cell adhesion and migration of gonoyctes toward the basement membrane.
まずExtended Data Figure 1aだね。aの注は以下だ。
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a, SNP patterns of STAP stem cells, Fgf4-induced stem cells and related ES cells as revealed by WGS. Chromosomes 1–19 and X are aligned from left to right. All cell lines and mouse strains except for STAP stem cell GLS1, GOF-ES and GOF-mouse are male. 129/GFP ES cells and the re-sequenced control DNA of STAP cells for ChIP-seq (Fig. 4 in ref. 2) are also shown. B6-homozygous, B6/129-heterozygous and 129-homozygous SNPs are shown in magenta, green and blue, respectively. Note that ntESG1 and ntESG2 inherited the B6-type X chromosome from maternal mice. Genomic regions in which FES1 and FES2 ES cells have different SNP clusters in chromosomes (chromosomes 6, 11 and 12) are marked by red rectangles. See b, c and Fig. 1b for a high-resolution map. SNP resolution is 10 Mb.
ここで、今我々が問題にしているGLS等のSNPsパターンは1,2と13段目だけどどこにも違いが分からないね。桂報告では親のSNPsパターンと違っていたというがどこで見分ければいいのかね。見分けられないものをデータとして持ってきたのかい?
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７）GOF マウスの SNPs 分布が、STAP 幹細胞 GLS1 および ES 細胞 GOF-ES の SNPs 分布と異 なっていたこと
さて、桂報告書の<X 染色体上の構造異常（大きな欠失＋末端重複逆位接続）>
或いはネイチャー報告"STAP cells are derived from ES cells"の、
< a large truncation with a terminal inverted repeat in one of two X chromosomes>
に物証がついていることをどう考えるかということになるね。
