松崎たちは6を怪しいと思ったから分析したんだよ。
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*The line subjected to WGS is indicated in parentheses in cases in which several sublines were established for one cell type. Other sublines were confirmed by PCR and sequencing.
Tsさんの最初の問題提起からね。
松崎たちはこの分析で具体的に何を分析したのかということね。
<STAP cells are derived from ES cells>のExtended Data Figure 2のCね。
Tsさんが言ってるのはAC129-1と129B6F1ES6とSTAP ChIP lysateの６番染色体の
SNIP比較が鮨されているが全部違ってるぞという指摘だわね。
Cの注は以下よ。内容的には桂報告にあることよね。
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c, Distribution of B6-type and 129-type SNPs along chromosome 6. The B6-homozygous SNP cluster (magenta) in the middle, which probably arose from the inheritance of the parental 129, is heterogeneous in length among six control ES cell lines. The four cag-GFP STAP stem-cell lines share the same length of the B6 SNP cluster with control ES 129B6F1 ES1. Note that the 129/B6-heterozygous SNP region in the 129 cag-GFP mouse is longer than that of AC129-1.
その支離滅裂な論理に対してTsさんはそれに構わず、図の結果だけに注目したのね。
①AC129-1
②129B6F1ES6
③STAP ChIP lysate
全部わずかに違ってるという指摘ね。そして①と③は同じだと言ってるんだろと
英語で書き込まれた。
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In Extended Data Figure 2.C, some differences are seen in Distribution of B6-type and 129-type SNPs between AC129-1 and STAP ChIP lysate.
Are these two cells the cells of the same individual?
そのSTAP ChIP lysate = 129B6F1ES1 の部分の説明は本文にあるのね。
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Control genomic DNA sequences for STAP cell chromatin immu-noprecipitation sequencing (ChIP-seq) experiments (Fig. 4 in ref. 2)had been deposited in the NCBI database2. To gain sufficient sequen-cing coverage, we re-sequenced the genomic DNA prepared from theSTAP cell lysate used for ChIP-seq (Extended Data Fig. 1a). We con-firmed that this STAP cell sample shared all the genomic character-istics described above for 129B6F1 ES1 (Extended Data Fig. 2c),indicating that the STAP cell sample used for ChIP-seq was derivedfrom 129B6F1 ES1 cells .
STAP細胞クロマチン免疫沈降シークエンシング（ChIP-seq）実験（Fig. 4 in ref. 2）のためのコントロールゲノムDNA配列はNCBIデータベースに登録されていた。 十分なシーケンシングカバレッジを得るために、我々はChIP-seqに使用したSTAP細胞溶液から調製したゲノムDNAを再配列決定しました（Extended Data Fig 1a）。 我々は、このSTAP細胞試料が、129B6F1ES1（Extended Data Fig. 2c）について上述した全てのゲノム特性を共有し、ChIP-seqに使用されるSTAP細胞試料が129B6F1 ES1細胞由来であることを示した。
そういうことなんだよ。そして更に、彼らは重大なごまかしをしている。
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しかも、肝心の129B6F1ES1 は、ゲノム解析されてないようで。
>The genome of 129B6F1 ES6 was sequenced, but further analysis showed that 129B6F1 ES1 rather than 129B6F1 ES6 shares all genomic anomalies found in AC129-1 (see main text).
本文からの引用文ではないのね。そこに対応する部分の本文は以下だわね。
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SNP analysis revealed that two independent STAP stem-cell lines,AC129-1 and AC129-2, had a 129B6F1 genetic background, whilethey were documented in the original article1as being establishedfrom 129 cag-GFP mice. We identified five heterozygous genomicanomalies: four deletions, and a duplication in these STAP stem-celllines (Extended Data Fig. 2b, d), which were not found in thesequenced parental mouse genomes. We identified that these anom-alies and sexual identity were shared by one of six control ES cell lineswith cag-gfp, 129B6F1 ES1, established earlier than AC129. This isalso the case for the other cag-GFP STAP stem-cell lines, FLS-T1 andT2, established in 2013. The 129B6F1 ES1 also shares a characteristichomozygous B6-SNP cluster in chromosome 6 with these four cag-GFP STAP stem-cell lines (Extended Data Fig. 2c, d). It is unlikely thatthe 129B6 ES1 line and these cag-GFP STAP stem-cell lines indepen-dently inherited all five chromosomal anomalies, the Y chromosome,and the same chromosome 6 from parental mice at establishment.
コピペで文字が繋がっちゃってるわね。やり直し。
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SNP analysis revealed that two independent STAP stem-cell lines,AC129-1 and AC129-2, had a 129B6F1 genetic background, while they were documented in the original article as being establishedfrom 129 cag-GFP mice. We identified five heterozygous genomicanomalies: four deletions, and a duplication in these STAP stem-celllines (Extended Data Fig. 2b, d), which were not found in the sequenced parental mouse genomes. We identified that these anomalies and sexual identity were shared by one of six control ES cell lines with cag-gfp, 129B6F1 ES1, established earlier than AC129. This is also the case for the other cag-GFP STAP stem-cell lines, FLS-T1 and T2, established in 2013. The 129B6F1 ES1 also shares a characteristic homozygous B6-SNP cluster in chromosome 6 with these four cag-GFP STAP stem-cell lines (Extended Data Fig. 2c, d). It is unlikely that the 129B6 ES1 line and these cag-GFP STAP stem-cell lines independently inherited all five chromosomal anomalies, the Y chromosome,and the same chromosome 6 from parental mice at establishment.
で、ここの論証自体は見事なんだけどね。肝心の129B6F1 ES1のデータが示されて
いないねとTsさんが指摘しているんだね。このSNIPと遺伝子異常はPCRで解析されていて
<肝心の129B6F1ES1 は、ゲノム解析されてないようで。>と言うのは事実で、WGSに
かけられたのは6だけだ。
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*The line subjected to WGS is indicated in parentheses in cases in which several sublines were established for one cell type. Other sublines were confirmed by PCR and sequencing.
とあって、表のカッコ内は6だ。
