| A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria
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Author:
Date:
2018-02-20
[Abstract] Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation and strand-specific sequencing of small RNA pools from bacteria that can be multiplexed to accommodate multiple biological samples in a single experiment. Small RNAs are isolated by polyacrylamide gel electrophoresis and treated with T4 polynucleotide kinase. This allows for 3’ adapter ligation to CRISPR RNAs, which don’t have pre-existing 3’-OH ends. Pre-adenylated adapters are then ligated using T4 RNA ligase 1 in the absence of ATP and with a high concentration of polyethylene glycol (PEG). The 3’ capture step enables precise determination of the 3’ ends of diverse RNA molecules. Additionally, a random hexamer in the ligated ...
[摘要] 新一代高通量测序技术能够对细胞中的RNA群体进行敏感和明确的分析。在这里，我们描述了一种从细菌中分离和链特异性测序小RNA池的方法，所述细菌可以在单个实验中多路复用以容纳多个生物样品。小RNA通过聚丙烯酰胺凝胶电泳分离并用T4多核苷酸激酶处理。这允许3'衔接头连接至CRISPR RNA，其不具有预先存在的3'-OH末端。然后使用T4 RNA连接酶1在不存在ATP和高浓度聚乙二醇（PEG）的情况下将前腺苷酸化的衔接子连接。 3'捕获步骤能够精确测定不同RNA分子的3'末端。此外，连接适配器中的随机六聚体有助于控制潜在的下游扩增偏差。逆转录后，将cDNA产物环化并通过PCR制备文库。我们显示扩增的文库不需要通过凝胶电泳可见，以期望产物的有效测序。使用这种方法，我们通常从少量纯化的小RNA制备RNA测序文库。该协议适合于通过对成熟的CRISPR RNA进行测序来测定细菌中的CRISPR RNA生物合成，但可以用于测序不同类型的小RNA。我们还提供了一个完整的数据处理管道示例，并提供了运行所提供脚本的说明。
【背景】与聚集的经常散布的短回文重复序列（CRISPR）相关的遗传模块赋予不同的原核宿主适应性免疫（Barrangou et ...
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| Extraction and Profiling of Plant Polar Glycerol Lipids
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Author:
Date:
2016-06-20
[Abstract] This protocol describes a method to extract total polar glycerol lipids from plant materials, followed by mass spectrometry profiling. Different glycerol lipid classes can be distinguished by their head-groups, which can be profiled automatically and quantitatively by a triple quadrupole mass spectrometry in multiple reaction monitoring (MRM) mode with an autosampler. Comparing with other established methods, such as thin layer chromatography (TLC) separation followed by Gas spectrometry (GC) analysis, this method requires little effort in sample preparation and separation, while the resolution is not limited to general lipid classes but at side chain level. This method was described and used successfully to profile plant lipids changes under freezing stress in Welti et al. ...
[摘要] 该方案描述了从植物材料提取总极性甘油脂质的方法，随后是质谱分析。 不同的甘油脂类可以通过其头基来区分，其可以通过使用自动进样器的多重反应监测（MRM）模式中的三重四极杆质谱自动和定量地进行概况分析。 与其他已建立的方法，例如薄层色谱（TLC）分离，然后气体光谱（GC）分析相比，该方法在样品制备和分离中几乎不需要付出努力，而分辨率不限于一般脂质类别，而是侧链水平 。 在Welti等人（2002）中描述并且成功地使用该方法来分析在冰冻胁迫下植物脂质的变化。
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