Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments
Semiautomated and rapid quantification of nucleic acid footprinting and structure mapping experiments
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DOI：
10.1038/nprot.2008.134
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发表时间：
2008-01-01
期刊：
影响因子：
14.8
通讯作者：
Altman, Russ B.
中科院分区：
文献类型：
--
作者：
Laederach, Alain;Das, Rhiju;Altman, Russ B.
我们已经开发了快速定量的单核苷酸分辨率的核酸化学作图凝胶带强度的协议。这些方案在软件SAFA（半自动足迹分析）中实现，该软件可以从http://safa.stanford.edu免费下载。在SAFA中实施的协议有五个步骤：（i）泳道识别，（ii）凝胶校正，（iii）条带分配，（iv）模型拟合和（v）条带强度归一化。SAFA能够快速定量包含数千个离散条带的凝胶图像，从而消除了化学作图实验分析的瓶颈。该软件的经验丰富的用户可以量化凝胶图像在类似于20分钟。虽然SAFA的开发是为了分析羟基自由基（中心点OH）足迹，它有效地量化与其他类型的化学映射探针获得的凝胶图像。我们还提供了一系列教程电影，说明SAFA分析中的最佳实践和不同步骤，作为该协议的补充。
We have developed protocols for rapidly quantifying the band intensities from nucleic acid chemical mapping gels at single-nucleotide resolution. These protocols are implemented in the software SAFA (semi-automated footprinting analysis) that can be downloaded without charge from http://safa.stanford.edu. The protocols implemented in SAFA have five steps: (i) lane identification, (ii) gel rectification, (iii) band assignment, (iv) model fitting and (v) band-intensity normalization. SAFA enables the rapid quantitation of gel images containing thousands of discrete bands, thereby eliminating a bottleneck to the analysis of chemical mapping experiments. An experienced user of the software can quantify a gel image in similar to 20 min. Although SAFA was developed to analyze hydroxyl radical (center dot OH) footprints, it effectively quantifies the gel images obtained with other types of chemical mapping probes. We also present a series of tutorial movies that illustrate the best practices and different steps in the SAFA analysis as a supplement to this protocol.