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Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency
Cell Stem Cell ( IF 23.9 ) Pub Date : 2018-12-06 , DOI: 10.1016/j.stem.2018.11.009
Kenjiro Adachi , Wolfgang Kopp , Guangming Wu , Sandra Heising , Boris Greber , Martin Stehling , Marcos J. Araúzo-Bravo , Stefan T. Boerno , Bernd Timmermann , Martin Vingron , Hans R. Schöler

(Cell Stem Cell23, 266–275.e1–e6; August 2, 2018) In our originally published article, input reads mapped to the mm9 rather than mm10 version of the mouse genome, which were prepared for a pilot analysis, were inadvertently used as controls for ChIP-seq peak calling. Those incorrect input files were used for peak calling to estimate background distribution, but they were not directly used for other downstream analysis, e.g., peak clustering. We have reanalyzed the data using the correct input reads aligned to mm10. This has reduced the number of significant peaks, mostly due to eliminating false positives (e.g., the cluster Esrrb c2 from the original version has disappeared), but it did not affect the overall results derived from the peak calling. We have now made changes to reflect this in Figures 2A, 2C–2E, S2F–S2I, S2L, and S2M; Table S3; the legend for Figure 2A (a corrected version of which also appears below the corrected version of the figure); and the processed mapping data deposited in ArrayExpress. Accordingly, a line of text in our Results section that formerly read, “The Esrrb binding sites (c1 and c3) were highly enriched for the cognate estrogen-related receptor (ERR) motif,” now reads, “The Esrrb binding sites (c1 and c2) were highly enriched for the cognate estrogen-related receptor (ERR) motif.” These changes do not affect the interpretation of the ChIP-seq results. We sincerely apologize for any confusion that this error may have caused.Figure 2Esrrb- and LIF-Dependent Remodeling of Core TF Occupancy during EpiSC Reprogramming (original)View Large ImageFigure ViewerDownload Hi-res imageDownload (PPT)Figure S2Esrrb and LIF Drive Remodeling of Core Transcriptional Networks, Related to Figures 1 and 2 and Tables S2–S4 (corrected)View Large ImageFigure ViewerDownload Hi-res imageDownload (PPT)Figure S2Esrrb and LIF Drive Remodeling of Core Transcriptional Networks, Related to Figures 1 and 2 and Tables S2–S4 (original)View Large ImageFigure ViewerDownload Hi-res imageDownload (PPT)

中文翻译:

Esrrb解锁沉默的增强子以重新编程为幼稚的多能性

(Cell Stem Cell23,266–275.e1-e6; 2018年8月2日)在我们最初发表的文章中,无意中使用了映射到小鼠基因组的mm9而不是mm10版本的输入读数,这些读数已准备进行初步分析作为ChIP-seq峰调用的控件。这些不正确的输入文件用于峰调用以估计背景分布,但未将它们直接用于其他下游分析,例如峰聚类。我们使用与mm10对齐的正确输入读数重新分析了数据。这减少了显着峰的数量,主要是由于消除了误报(例如,原始版本的Esrrb c2簇已消失),但它并未影响从峰调用得出的总体结果。现在,我们进行了更改以在图2A,2C-2E,S2F-S2I,S2L和S2M中反映出来;表S3;图2A的图例(其更正版本也出现在该图的更正版本下方);并将处理后的映射数据存储在ArrayExpress中。因此,我们的“结果”部分中的一行文字以前是“ Esrrb结合位点(c1和c3)高度富含相关雌激素相关受体(ERR)基序”,现在显示为“ Esrrb结合位点(c1和c2)高度丰富了相关的雌激素相关受体(ERR)基序。” 这些变化不会影响ChIP-seq结果的解释。对于此错误可能引起的任何困惑,我们深表歉意。
更新日期:2018-12-07
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