Supplementary File S2: Plasmids for independently tunable, low-noise gene expression

Supplementary File S2 README 2019-April-26 "Plasmids for independently tunable, low-noise gene expression" (Version 2) João P. N. Silva, Soraia Vidigal Lopes, Diogo J. Grilo, Zach Hensel This file describes the contents of the supplementary file for this manuscript. Python scripts were run in a Python 3 environment on OSX with various scientific python packages updated as of April 2019. With minor modifications for any similar environment it should be possible to generate Figures 1, 2, and 4 in the manuscript from these scripts and raw data. Contents: \dna sequences<br> \pDG101.gb Annotated DNA sequence in genbank format of plasmid pDG101<br> \pJS101.gb Annotated DNA sequence in genbank format of plasmid pJS101 (AddGene #118280)<br> \pJS102.gb Annotated DNA sequence in genbank format of plasmid pJS102 (AddGene #118281)<br> \pZH501.gb Annotated DNA sequence in genbank format of plasmid pZH501<br> \pZH509.gb Annotated DNA sequence in genbank format of plasmid pZH509 (AddGene #102664)<br> \pZH713.gb Annotated DNA sequence in genbank format of plasmid pZH713<br> \ZHX99.gb Annotated DNA sequence in genbank format for E. coli MG1655 chromosome insertion mutant ZHX99<br> <br> \data<br> \DG FCS Data: Raw flow cytometry data from BioRad S3 sorted by day and experimental condition; file name format: plasmid_inducer-concentration_inducer-units_inducer.fcs<br> \pJS101 pDG101 independence<br> \"quick scope intensity.ijm" Fiji macro used to extract average fluorescence intensities<br> \"Microscope Data\" Microscope data analyzed using the above Fiji macro; directory names indicate ATc and IPTG concentrations for each experimentation condition/replicate<br> \"intensity analysis\"<br> X_nM_ATc_Y_uM_IPTG.csv files: Exported CSV data from Fiji for each condition<br> backgrounds.csv: Average intensity for every condition, image frame, and color for background subtraction<br> \"images for Figure 4": Image stack with raw images used to generate Fig 4A and 4B \code<br> \fcsAnalysis_final_181228.py step-wise script for generating Figures 1 and 2 from FCS data<br> \fcsCalcDirectory181228.py script containing functions for FCS analysis and figure generation<br> \fcsImages PDF figures output by FCS analysis scripts<br> \FlowCal-master Distribution of the FlowCal library used in analysis for this manuscript; this is distributed under the MIT license<br> \scopeAnalysisWorkflow190430.py step-wise script for generating Figures 4C and 4D from cell fluorescence microscopy data in CSV format exported from Fiji<br> \scopeCalcDirectory190430.py script containing functions for microscopy data analysis and figure generation补充文件S2 说明文档 2019年4月26日 "可独立调控、低噪声的基因表达质粒（版本2）" 若昂·P·N·席尔瓦（João P. N. Silva）、索拉亚·维迪加尔·洛佩斯（Soraia Vidigal Lopes）、迪奥戈·J·格里洛（Diogo J. Grilo）、扎克·亨塞尔（Zach Hensel） 本文档说明本论文补充文件的组成内容。本研究所用Python脚本基于Python 3环境在OSX系统中运行，所用各类科学计算Python包均更新至2019年4月版本。仅需对同类环境进行少量适配修改，即可通过本脚本与原始数据复现论文中的图1、图2与图4。 内容目录： DNA序列 pDG101.gb：质粒pDG101的GenBank（GenBank）格式注释DNA序列 pJS101.gb：质粒pJS101的GenBank格式注释DNA序列（AddGene #118280） pJS102.gb：质粒pJS102的GenBank格式注释DNA序列（AddGene #118281） pZH501.gb：质粒pZH501的GenBank格式注释DNA序列 pZH509.gb：质粒pZH509的GenBank格式注释DNA序列（AddGene #102664） pZH713.gb：质粒pZH713的GenBank格式注释DNA序列 ZHX99.gb：大肠杆菌MG1655染色体插入突变株ZHX99的GenBank格式注释DNA序列 数据 DG流式细胞术（Flow Cytometry，FCS）数据：来自BioRad S3流式细胞仪的原始流式细胞术数据，按实验天数与实验条件分组；文件命名格式为：plasmid_inducer-concentration_inducer-units_inducer.fcs pJS101与pDG101独立性验证实验 "quick scope intensity.ijm"：用于提取平均荧光强度的Fiji宏脚本 "显微镜数据"：通过上述Fiji宏脚本处理的显微镜原始数据；目录名称标注了各实验条件/重复样本的ATc与IPTG浓度 "强度分析" X_nM_ATc_Y_uM_IPTG.csv：各实验条件下从Fiji导出的CSV格式数据 backgrounds.csv：用于背景扣除的各实验条件、图像帧与荧光通道的平均荧光强度数据 "图4原始图像"：用于生成图4A与4B的原始图像堆栈 代码 fcsAnalysis_final_181228.py：用于从流式细胞术数据生成图1与图2的分步脚本 fcsCalcDirectory181228.py：包含流式细胞术数据分析与图像生成相关函数的脚本 fcsImages：流式细胞术分析脚本生成的PDF格式图像文件 FlowCal-master：本研究分析所用的FlowCal工具库分发包，采用MIT许可证发布 scopeAnalysisWorkflow190430.py：用于从Fiji导出的CSV格式细胞荧光显微镜数据生成图4C与4D的分步脚本 scopeCalcDirectory190430.py：包含显微镜数据分析与图像生成相关函数的脚本