DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
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DOI：
10.1038/nmeth.2206
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发表时间：
2012-11
期刊：
影响因子：
48
通讯作者：
Lansdorp, Peter M.
中科院分区：
文献类型：
--
作者：
Falconer, Ester;Hills, Mark;Naumann, Ulrike;Poon, Steven S. S.;Chavez, Elizabeth A.;Sanders, Ashley D.;Zhao, Yongjun;Hirst, Martin;Lansdorp, Peter M.
姐妹染色单体交换（SCE）等DNA重排是基因组应激和不稳定性的敏感指标，但它们通常被单细胞测序技术掩盖。我们开发了Strand-seq来独立地对来自单细胞的亲本DNA模板链进行测序，从而能够以比以前更高的分辨率绘制SCE。平均而言，小鼠胚胎干细胞（mES）表现出8个SCE，检测到的分辨率高达23 bp。引人注目的是，62个单mES细胞的Strand-seq预测mm 9小鼠参考基因组组装包含至少17个方向错误的片段，总计近1%的基因组。这些错误定向的重叠群和片段在小鼠参考基因组的几次迭代中一直存在，并且难以使用常规测序技术检测。通过Strand-seq以高分辨率映射SCE事件和微调参考基因组的能力极大地扩展了单细胞测序的范围。
DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We developed Strand-seq to independently sequence parental DNA template strands from single cells, making it possible to map SCEs at orders-of-magnitude greater resolution than was previously possible. On average, murine embryonic stem (mES) cells exhibit eight SCEs, which are detected at a resolution of up to 23 bp. Strikingly, Strand-seq of 62 single mES cells predicts that the mm9 mouse reference genome assembly contains at least 17 incorrectly oriented segments totaling nearly 1% of the genome. These misoriented contigs and fragments have persisted through several iterations of the mouse reference genome and have been difficult to detect using conventional sequencing techniques. The ability to map SCE events at high resolution and fine-tune reference genomes by Strand-seq dramatically expands the scope of single-cell sequencing.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
64.8
作者：
Greaves, Mel;Maley, Carlo C.
通讯作者：
Maley, Carlo C.
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
64.8
作者：
Navin N;Kendall J;Troge J;Andrews P;Rodgers L;McIndoo J;Cook K;Stepansky A;Levy D;Esposito D;Muthuswamy L;Krasnitz A;McCombie WR;Hicks J;Wigler M
通讯作者：
Wigler M
影响因子：
64.5
作者：
Sakaue-Sawano, Asako;Kurokawa, Hiroshi;Miyawaki, Atsushi
通讯作者：
Miyawaki, Atsushi