This READ ME.txt file was generated on 26-11-2020 by Palma, C.S.D. GENERAL INFORMATION 1. Title of Dataset: Microscopy data 2. Author Information A. Principal Investigator Name: Andre S. Ribeiro Institution: Tampere University Email: andre.sanchesribeiro@tuni.fi 3. Date of data collection (range): [2017-02-21] - [2019-05-29] 4. Information about funding sources that supported the collection of the data: This work was supported by the Finnish Academy of Science and Letters [to C.P.]; Pirkanmaa Regional Fund [to V.K.]; Tampere University Graduate Program (Finland) [to V.C. and M.B.]; EDUFI Fellowship [TM-19-11105 to S.D.]; Academy of Finland [295027 to A.S.R.]; and Jane and Aatos Erkko Foundation [610536 to A.S.R.]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license. This releases your work to the public domain for any use. 2. Links to publications that use the data: https://www.sciencedirect.com/science/article/pii/S1874939919302615 3. Links to other publicly accessible locations of the data: https://sites.google.com/view/andreribeirolab/home/data-open-access 4. Citation for this dataset: C.S.D. Palma, V. Kandavalli, M.N.M. Bahrudeen, M. Minoia, V. Chauhan, S. Dash and A.S. Ribeiro (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. BBA - Gene Reg. Mech., 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515 DATA & FILE OVERVIEW 1. File List: Cell Morphology : Related to section 3.2 and 3.6 of [doi: 10.1016/j.bbagrm.2020.194515] Chromosome & Plasmid LacO3O1: Chromosome: Related to Fig.3 and Fig.4 of [doi: 10.1016/j.bbagrm.2020.194515] Plasmid: Related to Fig.3 of [doi: 10.1016/j.bbagrm.2020.194515] GyrA-YFP: Related to Fig.S8 of [doi: 10.1016/j.bbagrm.2020.194515] Nucleoid vs Gyrase: Related to section 3.3 and Table S4 of [doi: 10.1016/j.bbagrm.2020.194515] 2. Additional related data collected that was not included in the current data package: Microscopy data of different regions (xy) of microscopy slides for each condition can be made available upon request. 3. Are there multiple versions of the dataset? No METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Collection and data generation are described in Section 2.7 of "C.S.D. Palma et al. (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. BBA - Gene Reg. Mech., 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515" 2. Methods for processing the data: Data processing methods and the software packages used are described in Section 2.7 of "C.S.D. Palma et al. (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. BBA - Gene Reg. Mech., 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515" DATA-SPECIFIC INFORMATION FOR: [Cell Morphology] To test for mophological changes we measured cell areas in 3 different conditions. 1. Cases: Control: E.coli BW25993 100ug/ml Novobiocin: E.coli BW25993 subjected to 100ug/ml Novobiocin 0.4% Rhamnose: E. coli BW25993 harboring plasmid (pZe11 Prham gyrAB-sfGFP) subjected to 0.4% Rhamnose 2. Image type: Phase contrast images DATA-SPECIFIC INFORMATION FOR: [Chromosome & Plasmid LacO3O1] To measure the inverse of the mean rate of RNA production for the strain where PLacO3O1-mCherry-MS2-BS, is integrated into the lac locus of the genome and for the strain with PLacO3O1-mCherry-MS2-BS integrated into a single-copy F-plasmid. 1. Cases: Chromosome: Microscopy images of the strain with PLacO3O1-mCherry-MS2-BS integrated into the lac locus of the genome. Timeseries (15 min): Microscopy images taken every 15min Control: Cells not subject to Novobiocin Novobiocin: Cells subject to 100ug/ml Novobiocin Timeseries (1 min): Confocal Microscopy images taken every 1 min and Phase contrast images every 5min for 90 min of cells subject to 100ug/ml Novobiocin Plasmid: Microscopy images of the strain with PLacO3O1-mCherry-MS2-BS integrated into a single-copy F-plasmid. 0 : Confocal and Phase contrast images taken at 0 min after induction of the target gene 120: Confocal and Phase contrast images taken at 120 min after induction of the target gene 2. Image type: Confocal (C2) and Phase contrast (C1) images DATA-SPECIFIC INFORMATION FOR: [GyrA-YFP] To access the intracellular levels of Gyrase A proteins, we imaged a strain with a gyrA gene endogenously tagged with the YFP coding sequence [doi: 10.1126/science.1188308.] 1. Image type: Confocal (C2) and Phase contrast (C1) images DATA-SPECIFIC INFORMATION FOR: [Nucleoid vs Gyrase] Nucleoid visualization by DAPI staining at different levels of Gyrase overexpression 1. Cases: 0 Rhamnose: Control condition (0% Rhamnose) 0.2% Rhamnose: Cells subject to Gyrase overexpression (0.2 % Rhamnose) 2. Image type: Confocal (C2) and Phase contrast (C1) images