One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics.
One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics.
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DOI：
10.1186/s13072-021-00427-2
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发表时间：
2021-12-11
影响因子：
3.9
通讯作者：
Pradhan S
中科院分区：
文献类型：
--
作者：
Vishnu US;Estève PO;Chin HG;Pradhan S
可分离的染色质景观允许转录因子的结合，以及在发育过程中启动子和增强子元件的重塑。染色质可及性沿着整合的多组学方法已用于确定患者样品中癌症的分子亚型。One-pot Universal NiceE-seq（One-pot UniNiceE-seq）是一种改进的可访问的染色质分析方法，其在文库制备之前否定DNA纯化并掺入无超声处理的酶促片段化，并且适用于各种哺乳动物细胞。One-pot UniNiceE-seq是通用的，能够在低至25个固定细胞中分析4%甲醛固定的染色质。与Tn 5转座子介导的方法相比，使用一锅法UniNiceE-seq在甲醛固定的细胞上的染色质谱更有效，证明了其多功能性。One-pot UniNiceE-seq允许在4%甲醛交联条件下在一锅中进行染色质标记和富集的整个过程。与其他技术相比，它不需要酶滴定，因为可接近的染色质被5 mC掺入标记，并通过切口酶阻止降解，从而为自动化打开了可能性。在线版本包含补充材料，可通过10.1186/s13072-021-00427-2获得。
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples. One-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility. One-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn’t require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation. The online version contains supplementary material available at 10.1186/s13072-021-00427-2.
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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：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
DOI：
10.1016/j.bbagrm.2014.03.001
发表时间：
2014-08
影响因子：
4.7
作者：
Rothbart, Scott B.;Strahl, Brian D.
通讯作者：
Strahl, Brian D.
影响因子：
0.8
作者：
Herrmann, Christin;Avgousti, Daphne C.;Weitzman, Matthew D.
通讯作者：
Weitzman, Matthew D.
影响因子：
5.7
作者：
Chin HG;Sun Z;Vishnu US;Hao P;Cejas P;Spracklin G;Estève PO;Xu SY;Long HW;Pradhan S
通讯作者：
Pradhan S