Gene syntax defines supercoiling-mediated transcriptional feedback

Data for "Gene syntax defines supercoiling-mediated transcriptional feedback" This includes all of the data required to compile and build the figures.See the listed Github repository (archived through Zenodo) for code generation files. The link is listed in the published paper. Zenodo deposit details The zenodo deposit contains four files: README.md (this file, also included in the data zip) gene_syntax_supercoiling_data.7z (all of the data to make all paper figures) plasmids.zip (plasmid sequences, in GenBank format for all plasmids) software.zip (a snapshot of https://github.com/GallowayLabMIT/tangles_experimental, the related software to process this data) For a higher compression ratio, the main data is compressed as a 7zip file instead of a zip file. Modern versions of Windows and MacOS are able to open this compressed file directly. If this doesn't work, the 7zip software is free and open-source and available at https://www.7-zip.org/ Data zip details The data zip contains the following data: Processed sequencing data in NGS_DATA/tangles_experimental, split by experiment type. Plasmid metadata needed for plotting in projects Flow data in instruments/data/attune and instruments/data/collaborators Microscopy data in instruments/data/keyence Antibody plate-reader data in instruments/data/plate_reader qPCR data in instruments/qPCR ddPCR data in instruments/Weiss.lab.ddPCR Using this data The Galloway lab uses a Python package called rushd to easily import datato make figures. If you want to reproduce figure plotting, the steps are: Unzip this data deposit to any deposit. Copy the full, absolute path to this folder, e.g. the folder containing README.md on Windows, this might look like C:\Users\username\Downloads\gene_syntax_supercoiling_data on MacOS, this might be \home\username\Downloads\gene_syntax_supercoiling_data on Linux, it might be \home\username\Downloads\gene_syntax_supercoiling_data git clone or otherwise download the code for this paper to a folder. Create a datadir.txt file with the path above, in the root of the code directory (e.g. at the same level of the README.md in the code repository). This should really be a single-line file containing only the path above! Create a Python virtual environment using the requirements.txt file. Run the Jupyter notebooks in the figures/ subdirectory.