遠藤さんはこれを解析して８番染色体上にトリソミーがあると予測した。
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Figure 3. Trisomy detected by SNP analysis of RNA-seq data. (A) Allele frequency distributions of whole chromosomes and chromosome 8. Only chromosome 8 of STAP cells had a peak that was not centered approximately 50%, indicating that chromosome 8 originating from the 129 strain was duplicated to produce trisomy of the chromosome. Unlike the RNA-seq data analyzed in Figs 1 and 2, the RNA-seq data analyzed in this figure were generated using the SMARTer reagent kit. (B) Expression analysis by chromosome. Only genes on chromosome 8 were significantly more expressed, and genes on chromosome 13 were significantly less expressed. P-values were calculated using two-sided Student t-tests.
こちらもやっと戻ってきたわね。
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Surprisingly, FI-SCs that were annotated as coming from the F1 129Sv (129) and B6 cell populations did not show the allele distribution pattern of unbiased nonimprinting genes (Fig. S1 in Supporting Information). The distribution was more similar to that of cells with unequal chromosomes. These FI-SCs were reported to be induced from STAP cells with Fgf4 and to have characteristics similar to trophoblast stem cells (TSCs), such as their gene expression profiles and potential to contribute to the placenta (Obokata et al. 2014a).
The obvious difference in the FI-SC curve from the 129B6F1 genotype, combined with the fact that the majority of SNPs were similar to B6, suggested that the FI-SCs originated from neonatal mice of a nearly pure B6 background. Further analysis of gene expression patterns suggested that the heterogeneity of SNPs between B6-type allele and non-B6 could be caused by the expression characteristics of genes. As shown in Fig. 2B, SNPs expected to be heterogeneous between 129 (i.e., non-B6) and B6 were examined in several ESC marker genes. ESCs carried alleles from both the 129 and B6 backgrounds at these loci, but the FI-SCs, although described as having the same genetic background as the ESCs (Obokata et al. 2014a), carried only SNPs from B6. This dominance of the B6 genotype was not observed in TSC marker genes (Fig. 2C).
和モガさんの返事はこうだよ。
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Re: No title
混入偽装だからこそ、論文とは違う系統になるんです。
混入偽装をしようとすると、既にその系統のES細胞が若山研にないといけない。小保方氏はES細胞を作れないので、このES細胞を使って捏造したというためです。例えば、若山氏が市販129X1マウス×若山B6マウスでSTAP細胞を作らせようとすると、129B6F1 CAG-GFPヘテロのSTAP細胞が出来ますが、この系統のES細胞は若山研にはない。それでは困るから、マウスを既存のES細胞に合うように若山B6マウスを岡部B6マウスにすり替えることになります。従って、論文に書かれた129B6F1 CAG-GFPヘテロとは違う129B6F1 Acr/CAG-GFPヘテロのSTAP関連細胞ができることになります。
2017.07.14 Fri l wamoga. URL l 編集
はい、貼っといてあげるわ。
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Re: No title
質問の意味は10月頃からSTAP実験が本格化したとすると、どう早くても最初のキメラとSTAP幹細胞ができるのは11月末になる。「混入偽装」だとその間に最初のキメラとSTAP幹細胞ができたとしているので時間的には無理だという意味に受け取っています。
まず、この10月頃というのは小保方氏の記憶違いではないかと思います。若山氏が「動物実験承認申請書」を提出したのは9月9日なので、若山氏がSTAP実験を本格的化させたのはこの辺りだと思います。あと、若山氏が今日からマイクロナイフで切って入れようと思いついたのは、キメラの結果を見た後ではない可能性があります。「②何度か試す移植に3日」の3日間のある日、突然閃いた可能性があります。この場合、最初のキメラとSTAP幹細胞が出来るのは20日程早まります。
若山氏は最初のキメラ、STAP幹細胞を作ったときには対応するES細胞はなかったと言っています。STAP幹細胞GLSの樹立は11月25日ですが、これには対応するGOF-ESがありますので、最初の129B6F1のキメラ、STAP幹細胞は11月25日以前に出来ていることになります。
2017.07.17 Mon l wamoga. URL l 編集
あら上は私よ。
ついでに、
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Surprisingly, FI-SCs that were annotated as coming from the F1 129Sv (129) and B6 cell populations did not show the allele distribution pattern of unbiased nonimprinting genes (Fig. S1 in Supporting Information). The distribution was more similar to that of cells with unequal chromosomes. These FI-SCs were reported to be induced from STAP cells with Fgf4 and to have characteristics similar to trophoblast stem cells (TSCs), such as their gene expression profiles and potential to contribute to the placenta (Obokata et al. 2014a).
The obvious difference in the FI-SC curve from the 129B6F1 genotype, combined with the fact that the majority of SNPs were similar to B6, suggested that the FI-SCs originated from neonatal mice of a nearly pure B6 background. Further analysis of gene expression patterns suggested that the heterogeneity of SNPs between B6-type allele and non-B6 could be caused by the expression characteristics of genes. As shown in Fig. 2B, SNPs expected to be heterogeneous between 129 (i.e., non-B6) and B6 were examined in several ESC marker genes. ESCs carried alleles from both the 129 and B6 backgrounds at these loci, but the FI-SCs, although described as having the same genetic background as the ESCs (Obokata et al. 2014a), carried only SNPs from B6. This dominance of the B6 genotype was not observed in TSC marker genes (Fig. 2C).
TSさんが確認しているのは遠藤さんのトリソミー結論で、今分析結果が
感想の奴と同じだった→X。やっとアライメントが1つ終わったところ。ChipのBowtie2によるアライメント率は97､8%、Tru-SeqがTophat2で85,6%,そしてSMARTERが4､5日かかって73%だ。そのアライメント率が感想氏のやったマッピングのアライメント率同じだったということ。
73%ということは、3割のリードが捨てられる。定性的なことは言えても、果たして統計計算にしてもいいものか、そもそも論だね。
By Ts.Marker
