Phenotypic profiling data for elucidating genomic gaps|基因组学数据集|代谢工程数据集

Dataset 1. Raw OD600 growth curves (raw_od_curves.csv).MAPs optical density measurements from the plate reader for 96 wells. Numbered headers indicate the time (hrs) and the column contents indicate the OD600 measurement.Dataset 2. Parameters for logistic curves (curve_logistic_parameters.csv).Lag, maximum growth rate, and carrying capacity parameters for the 96 wells. Sum-squared error and growth level are included.Dataset 3. C.sedlakii KBase phenotypes (c.sedlakii_phenotypes.csv).Phenotype csv file required for KBase phenotype simulations. This file specifies media data object name, the KBase workspace, and growth. The gene knockout and additional compound columns were not used and set to none.Dataset 4. (C. sedlakii_nogapfill.sbml)The initial metabolic model of Citrobacter sedlakii built solely from the functional annotations.Dataset 5.  (C.sedlakii_ArgonneLB_gapfill.sbml)The initial metabolic model of Citrobacter sedlakii with reactions identified by the gap-fill algorithm on the LB media
condition.Dataset 6. (C.sedlakii_MAP_gapfill.sbml)The LB-gap-filled model with reactions identified by
the gap-fill algorithm on the MAPs media conditions.

数据集1：原始OD600生长曲线（raw_od_curves.csv）。该数据集包含来自96孔板读数仪的MAPs光学密度测量值。编号的表头指示时间（小时），而列内容则表明OD600测量值。数据集2：逻辑曲线参数（curve_logistic_parameters.csv）。包含96孔板的最大生长速率、承载能力参数以及滞后时间，并包括了均方误差和生长水平。数据集3：C.sedlakii KBase表型（c.sedlakii_phenotypes.csv）。此csv文件为KBase表型模拟所必需的表型数据文件，其中指定了培养基数据对象名称、KBase工作空间以及生长情况。基因敲除和附加化合物列未被使用，并设置为“无”。数据集4：（C. sedlakii_nogapfill.sbml）仅基于功能注释构建的Citrobacter sedlakii的初始代谢模型。数据集5：（C.sedlakii_ArgonneLB_gapfill.sbml）在LB培养基条件下，通过gap-fill算法识别反应的Citrobacter sedlakii初始代谢模型。数据集6：（C.sedlakii_MAP_gapfill.sbml）在LB-gap-filled模型基础上，通过gap-fill算法在MAPs培养基条件下识别反应的代谢模型。