1、单细胞多组学测序方法scGTP-seq 文章标题:Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells 发表期刊:Clinical and Translational Medicine(IF=10.6) 文章链接:https://doi.org/10.1002/ctm2.1351 癌细胞往往表现...
2 eccDNA的三代基因测序(Third-generation sequencing, TGS)检测技术 三代基因测序(Third-generation sequencing, TGS)检测技术又称长读长基因测序技术,相较于NGS短读长的不足,TGS很好地弥补了由于短读长特点导致的数据拼接困难、对拷贝数...
云序生物有幸参与了该项研究当中的eccDNA 测序以及数据分析工作。 论文标题:Whole-genome sequencing of extrachromosomal circular DNA of cerebrospinal fluid of medulloblastoma 发表期刊:Frontiers in Oncology(5.738) 发表日期:2022 年 11 月 08 日 实验方法:组织细胞环状 DNA 测序、体液样品环状 DNA 测序、 1、MB...
目前针对eccDNA的实验方法主要有两种,一种是参考“Circle-Seq: Isolation and Sequencing of Chromosome-Derived Circular DNA Elements in Cells”[1]进行的滚环扩增法(RCA),还有一种是参考卢煜明教授“Identification and characterization of extrachromosomal circular DNA in maternal plasma ”[2]的Tn5酶切法,两种方案...
在第一种测序方法当中,由于采用了全读长的单分子纳米孔测序(Oxford Nanopore sequencing),故可检测出单个 eccDNA 是否由基因组不同位置来源的多个片段拼接而成——结果显示,虽然绝大多数 eccDNA 仅来自单个基因组片段,但确实存在少量 eccDNA 来自多于一个的基因组位置,甚至存在 3 个 eccDNA 由多达七个不同来源的基...
建库 1)用超声仪将扩增产物片段化为300bp–500bp; 2)用SMARTer PrepX DNA Library Kit或其它kit进行建库。 参考文献 Henrik Devitt Møller Circle-Seq: Isolation and Sequencing of Chromosome-Derived Circular DNA Elements in Cell
As control data a variety of sequencing data can be provided for use (e.g. rRCA enriched data from a different ecotype or tissue, non-enriched data, or WGS (whole genome sequencing) data). Using both control data and a reference genome sequence, the ECCplorer yields the most reliable ...
In particular, low‐copy‐number LTR‐RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3 , ...
H.C. generated the ligase-knockout cell lines; M.W. developed the method to call eccDNA from Nanopore data and performed all bioinformatics analyses; M.N.D. performed pilot analysis of eccDNA sequencing data; D.L. helped with the SAFM imaging; F.W.A. supervised the work by H.C.; Y...
2021年8月23日,华大基因唐冲博士团队在表观遗传与染色质研究权威期刊Epigenetics & Chromatin上发表题为"Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure"的论文,开发出一种单分子层级研究ecDNA染色质开放性的新技术 —— CCDA-seq。 尐尐...