Protocol for assay of transposase accessible chromatin sequencing in non-model species.
Protocol for assay of transposase accessible chromatin sequencing in non-model species.
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DOI：
10.1016/j.xpro.2021.100341
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发表时间：
2021-03-19
期刊：
影响因子：
--
通讯作者：
Orsini L
中科院分区：
文献类型：
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作者：
Kissane S;Dhandapani V;Orsini L
转座酶可及染色质分析 (ATAC-seq) 是一种绘制全基因组染色质可及性图谱的方法。与高通量测序相结合，它可以实现综合表观基因组分析。 ATAC-seq 需要直接进入细胞核，这对于小型无脊椎动物等非模型物种来说是一个重大挑战，因为它们的软组织被保护性外骨骼包围。在这里，我们提出了针对小型甲壳类动物应用的 ATAC-seq 协议的修改，将应用扩展到非模型物种。有关该协议的使用和执行的完整信息，请参阅。 ATAC-seq 修改方案适用于非模式物种应用 转座酶滴定以较低的成本确定最佳转座的阈值 确定低输入反应的最小数量的细胞/组织 水蚤 ATAC-seq 分析大型水蚤的概念验证 转座酶可及染色质测定 (ATAC-seq) 是一种绘制全基因组染色质可及性图谱的方法。与高通量测序相结合，它可以实现综合表观基因组分析。 ATAC-seq 需要直接进入细胞核，这对于小型无脊椎动物等非模型物种来说是一个重大挑战，因为它们的软组织被保护性外骨骼包围。在这里，我们提出了针对小型甲壳类动物应用的 ATAC-seq 协议的修改，将应用扩展到非模型物种。
The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses. ATAC-seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, whose soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-seq protocol for applications in small crustaceans, extending applications to non-model species. For complete information on the use and execution of this protocol, please refer to. ATAC-seq modified protocol for applications in non-model species Transposase titration identifies thresholds for optimal transposition at lower costs Minimal number of cells/tissue is identified for low input reactions Proof of concept ATAC-seq analysis for the waterflea Daphnia magna The assay for transposase accessible chromatin (ATAC-seq) is a method for mapping genome-wide chromatin accessibility. Coupled with high-throughput sequencing, it enables integrative epigenomics analyses. ATAC-seq requires direct access to cell nuclei, a major challenge in non-model species such as small invertebrates, whose soft tissue is surrounded by a protective exoskeleton. Here, we present modifications of the ATAC-seq protocol for applications in small crustaceans, extending applications to non-model species.