Genome alignments for 'Machine-driven parameter-space exploration of biochemical reactions'

The development of complex, multi-step <em>omics</em> methods in molecular biology is a laborious, costly, iterative and often intuition-bound process where an optimum is sought in a parameter space through step-by-step optimisations. The the difficulty of miniaturising assays and the cost of the experiments limit the dynamic range and the number of parameters that can be explored. However, because of non-linearities of the response of biochemical systems to their reagent concentrations, a broad dynamic range is necessary. Here we demonstrate the use of a high-performance nanoliter handling platform (Labcyte Echo 525) and computer generation of liquid transfer programs to explore in quadruplicates more than 600 combination of 4 parameters of a biochemical reaction, which lead us to uncover non-linear responses, parameter interactions and novel mechanical insights. With the increased availability of « <em>cloud biology</em> » computer-driven laboratory platforms, our results participate in changing methods development for biotechnology towards reproducible, computer-aided exhaustive characterisation of biochemical systems. This dataset contains the sequence alignments and other processing files produced by running the raw data (10.5281/zenodo.1680999) through a processing pipeline using the MOIRAI workflow manager. The most important output is the "CAGEscan_fragments" directories and represent the alignment of single mRNA molecules, which can be further analysed using the "CAGEr" software package available from Bioconductor. Run IDs: 171227_M00528_0321_000000000-B4GLP, 180123_M00528_0325_000000000-B4PCK, 180326_M00528_0346_000000000-B4GJR, 180403_M00528_0348_000000000-B4GP8, 180411_M00528_0351_000000000-BN3BL, 180501_M00528_0359_000000000-B4PJY, 180517_M00528_0364_000000000-BRGK6 180606_M00528_0367_000000000-BN3FG, 180607_M00528_0368_000000000-BN9KM分子生物学中复杂、多步骤的组学（omics）方法开发是一项费力、高成本、迭代且常依赖经验直觉的过程，需通过逐次优化在参数空间中探寻最优解。小型化检测的难度与实验成本限制了可探索的动态范围与参数数量。然而，由于生化系统对试剂浓度的响应存在非线性特性，宽广的动态范围实为必要。本研究展示了利用高性能纳升级液体处理平台（Labcyte Echo 525）与计算机生成的液体转移程序，对生化反应的4项参数进行四次重复实验，探索超过600种参数组合，进而揭示了非线性响应、参数交互作用与全新的机制见解。随着“云生物学（cloud biology）”计算机驱动实验室平台的日益普及，本研究成果推动生物技术的方法开发转向可重复、计算机辅助的生化系统全面表征。本数据集包含通过MOIRAI工作流管理器处理原始数据（10.5281/zenodo.1680999）所生成的序列比对文件与其他处理文件。其中最为核心的输出为“CAGEscan_fragments”目录，其包含单条mRNA分子的比对结果，可通过Bioconductor平台提供的“CAGEr”软件包进行后续分析。运行编号如下：171227_M00528_0321_000000000-B4GLP、180123_M00528_0325_000000000-B4PCK、180326_M00528_0346_000000000-B4GJR、180403_M00528_0348_000000000-B4GP8、180411_M00528_0351_000000000-BN3BL、180501_M00528_0359_000000000-B4PJY、180517_M00528_0364_000000000-BRGK6、180606_M00528_0367_000000000-BN3FG、180607_M00528_0368_000000000-BN9KM