本文は以下だね。
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To investigate the relationship among STAP cells, STAP stem cells, Fgf4-induced stem cells, ES cells and trophoblast stem cells, we performed genome-wide RNA-sequencing analysis (Fig. 2i for dendrogram; Extended Data Figs 3 and 4 for expression analyses of representative genes ; Supplementary Tables 2 and 3 for analysis conditions). Whereas STAP cells formed a cluster with STAP stem cells, Fgf4-induced stem cells, ES cells and trophoblast stem cells and not with the parental CD45+ cells, STAP cells were an outlier to the rest of the cell types in the cluster. In contrast, STAP stem cells were closely clustered with ES cells. Fgf4-induced stem cells formed a cluster with a sub-cluster of ES cells and STAP stem cells, whereas trophoblast stem cells comprised an outlier to this cluster, indicating a close relationship of Fgf4-induced stem cells with these pluripotent cells.
お気に入りは変化なしよ。
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１２）Letter Fig.2i 、Extended Data Fig.6dについて
Letter Fig.2iは2012年にTruseqによるRNA-seqを行い、そのデータに基づいて作成し た系統樹と考えられるが、論文の図では系統樹の一部が除かれている点
Letter Extended Data Fig.6dは、2012年にSMARTERキットによるRNA-seqを行い、その データをもとに作成した系統樹と考えられるが、このとき解析結果を返された際には Callus1（当時のCDB若山研の命名法ではSTAP細胞1という意味）と名付けられていた試 料が、Letter ではCD45+となっている点
三誌論文には幹細胞化の実験のことは書かれていないからね。まさに8月に提出する以前の
作業に関して語っているんだね。ここはどうなの?
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Letter Fig.2iは2012年にTruseqによるRNA-seqを行い、そのデータに基づいて作成し た系統樹と考えられるが、
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Letter Extended Data Fig.6dは、2012年にSMARTERキットによるRNA-seqを行い、その データをもとに作成した系統樹と考えられるが、
リジェンドは以下だね。
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3. Extended Data Figure 3: Transcriptome analyses of STAP cells shown by heat maps. (494 KB)
a, Heat maps of expression profiles of top-ranked up- and downregulated genes in STAP cells (Oct4-GFP+ clusters converted from CD45+ cells) compared to ES cells. Their respective expression levels in STAP stem cells, trophoblast stem cells and Fgf4-induced stem cells are shown. Absolute expression values are scaled by log2. The genes expressed differentially between ES cells and STAP cells tended to show more similar expression profiles to ES cells in STAP stem cells and Fgf4-induced stem cells than in trophoblast stem cells. Expression of some early endodermal lineage genes such as Gata4 and Sox17 was moderately elevated in STAP cells as compared to ES cells, whereas its biological significance remains elusive (these genes are shown to be strongly expressed in Oct4-GFP-dim cells1). b, Heat maps of expression profiles of top-ranked up- and downregulated genes in ES cells compared to CD45+ cells and their respective expression levels in STAP cells.
The genes expressed differentially between CD45+ and ES cells tended to show similar expression profiles in ES cells and STAP cells. c, Heat maps of expression profiles of representative genes implicated in haematopoietic lineage development in CD45+, ES and STAP cells. No strong correlation was seen between CD45+ cells and STAP cells in their expression profiles (a similar tendency of no correlation was seen for the data in b).
分かりにくいのはaとbとで遺伝子の並びが違うことだね。もう一度本文を見てみよう。
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To investigate the relationship among STAP cells, STAP stem cells, Fgf4-induced stem cells, ES cells and trophoblast stem cells, we performed genome-wide RNA-sequencing analysis (Fig. 2i for dendrogram; Extended Data Figs 3 and 4 for expression analyses of representative genes ; Supplementary Tables 2 and 3 for analysis conditions). Whereas STAP cells formed a cluster with STAP stem cells, Fgf4-induced stem cells, ES cells and trophoblast stem cells and not with the parental CD45+ cells, STAP cells were an outlier to the rest of the cell types in the cluster. In contrast, STAP stem cells were closely clustered with ES cells. Fgf4-induced stem cells formed a cluster with a sub-cluster of ES cells and STAP stem cells, whereas trophoblast stem cells comprised an outlier to this cluster, indicating a close relationship of Fgf4-induced stem cells with these pluripotent cells.
