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This data is distributed under the license CC BY NC 3.0 (https://creativecommons.org/licenses/by-nc/3.0/deed.en_GB). The data is preprocessed.
EMPIRICAL DATA ORGANIZED ACCORDING TO OUR PUBLICATIONS
DATA SET 14. Related to: R Jagadeesan, S Dash, CSD Palma, ISC Baptista, V Chauhan, J Mäkelä, and AS Ribeiro (2025) Dynamics of bacterial operons during genome-wide stresses. Science Advances 11 (20), eadl3570. DOI: 10.1126/sciadv.adl3570
Data Availability: https://datadryad.org/dataset/doi:10.5061/dryad.zgmsbccks;
DATA SET 13. Related to: Baptista ISC, Dash S, Arsh AM, Kandavalli V, Scandolo CM, Sanders BC, and Ribeiro AS (2025) Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses. PLoS Comput Biol 21(2): e1012817. https://doi.org/10.1371/journal.pcbi.1012817
Data Availability: https://doi.org/10.5061/dryad.dz08kps5n; Software: https://doi.org/10.5281/zenodo.14746159; Supplemental information: https://doi.org/10.5281/zenodo.14746189.
DATA SET 12. Related to: V Chauhan, ISC Baptista, A Arsh, R Jagadeesan, S Dash, and AS Ribeiro (2024) Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation. Biochemistry 63(16), 2009–2022. DOI: 10.1021/acs.biochem.4c00012.
Data Availability: A data package is deposited in Dryad with flow cytometry data, spectrophotometry data, and the constructs sequences and maps. The data are available at the link: https://doi.org/doi:10.5061/dryad.jm63xsjgt. The constructs will be available for distribution in Addgene.
DATA SET 11. Related to: S Dash, R Jagadeesan, ISC Baptista, V Chauhan, V Kandavalli, SMD Oliveira and AS Ribeiro (2023) A library of reporters of the global regulators of gene expression in Escherichia coli. mSystems, e00065-24. DOI: https://doi.org/10.1128/msystems.00065-24.
Data Availability: A data package was deposited in Dryad with flow cytometry, microscopy, and spectrophotometry data (doi:10.5061/dryad.b2rbnzsm8) - https://datadryad.org/stash/dataset/doi:10.5061/dryad.b2rbnzsm8. The library of GR reporters is available for distribution in Addgene.
DATA SET 10. Related to: S Dash*, CSD Palma*, ISC Baptista, MNM Bahrudeen, BLB Almeida, V Chauhan, R Jagadeesan and AS Ribeiro (2022) Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Research DOI: 10.1093/nar/gkac643. *Equal contributions.
Supplementary Data are available at NAR Online.
Data Availability: RNA-seq *.fastq data and processed data under cold shock and novobiocin are deposited in NCBI GEO with accession code GSE194037. Some raw RNA-seq data (control) was used before. Please access it using the NCBI GEO accession code GSE183139. Another data package was deposited in Dryad with flow-cytometry, microscopy, and plate reader data. (DOI: 10.5061/dryad.pvmcvdnnm).
DATA SET 9. Related to: B Almeida, MNM Bahrudeen*, V Chauhan*, S Dash*, V Kandavalli, A Häkkinen, J Lloyd-Price, CSD Palma, ISC Baptista, A Gupta, J Kesseli, E Dufour, O-P Smolander, M Nykter, P Auvinen, HT Jacobs, SMD Oliveira, and AS Ribeiro (2022) The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Research 50 (12), 6801-6819, DOI: 10.1093/nar/gkac540.
Data Availability: RNA-seq *.fastq data (trimmed) and processed RNA-seq data are deposited in NCBI GEO with accession code GSE178281 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178281). The raw data of the control condition (180 min, LB 1.0x ) was also used in (72) (GSE183139). In Dryad, we deposited a package with flow-cytometry, microscopy, spectrophotometry, and western blot data (DOI: 10.5061 / dryad.wh70rxwnp). The package also has two *.xlsx files informing on the genes TFN topological and logical parameters, RNA-seq expression, global network topological features, gene-gene interactions, and the lists of pairs of genes separated by path lengths from 1 to 8.
DATA SET 8. Related to: ISC Baptista*, V Kandavalli*, V Chauhan, MNM Bahrudeen, BLB Almeida, CSD Palma, S Dash, and AS Ribeiro (2022) Sequence-dependent model of genes with dual σ factor preference, Biochim. Biophys. Acta Gene Regul. Mech. 1865(3), 194812. DOI: 10.1016/j.bbagrm.2022.194812. BioRxiv: DOI:10.1101/2021.11.17.468920. *Equal contributions.
Data Availability: RNA-seq *.fastq data and processed RNA-seq data are deposited in NCBI GEO with accession code GSE188752 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188752). A data package was deposited in Dryad containing flow cytometry, microscopy and spectrophotometry data. The data is accessible through this link: https://doi.org/10.5061/dryad.jsxksn0b7.
DATA SET 7. Related to: Chauhan V*, Bahrudeen MNM*, Palma CSD, Baptista ISC, Almeida BLB, Dash S, Kandavalli V, and Ribeiro AS (2022) Analytical kinetic model of native tandem promoters in E. coli. PLOS Computational Biology , 18(1): e1009824. DOI: 10.1371/journal.pcbi.1009824. * Equal Authorship
Data Availability: A data package was deposited in Dryad under the DOI:10.5061/dryad.bnzs7h4bs. It contains the flow-cytometry and microscopy data, along with the MATLAB, R and Python codes used. Meanwhile, RNA-seq data is deposited in NCBI GEO with the accession code GSE183139.
DATA SET 6. Related to: CSD Palma, V Kandavalli, MNM Bahrudeen, M Minoia, V Chauhan and AS Ribeiro (2020) Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1863(5), 194515. doi: 10.1016/j.bbagrm.2020.194515. https://www.sciencedirect.com/science/article/pii/S1874939919302615
Microscopy data (IMAGES: single-cell RNA numbers, single-cell GyrA-YFP, single-cell nucleoids tagged with DAPI): https://datadryad.org/stash/share/0XPyj3KnyAMqCDMX78bElYXSQWhhcY13DT0lLEY2IbU
Flow cytometry data (single-cell fluorescence): http://flowrepository.org/id/FR-FCM-Z35A
DATA SET 5. Related to: MNM Bahrudeen*, V Chauhan*, CSD Palma, SMD Oliveira, VK Kandavalli, and AS Ribeiro (2019) Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. Journal of Microbiological Methods 166, 105745. DOI: 10.1016/j.mimet.2019.105745 *Equal contributions. https://www.sciencedirect.com/science/article/pii/S0167701219304889
Microscopy data (single-cell RNA numbers): https://drive.google.com/file/d/1QILwEQ6LBJvUoePUEHVb6qXVsqJux_Tp/view?usp=sharing
Flow cytometry data (single-cell fluorescence): https://drive.google.com/file/d/1fC7wnFGTwA23Owy1vX_sL_860ttMo6VO/view?usp=sharing
DATA SET 4. Related to: S Startceva, VK Kandavalli, A Visa, and AS Ribeiro (2019) Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1862(2), 119–128. DOI: 10.1016/j.bbagrm.2018.12.005. https://www.sciencedirect.com/science/article/pii/S1874939918304516
Microscopy (single-cell RNA numbers time series, mutant promoters): https://drive.google.com/file/d/1kld0h8a8WQRf-RPraTRQmOnopr5ra1z7/view?usp=sharing
DATA SET 3. Related to: MK Prajapat, AS Ribeiro (2018) Added value of autoregulation and multi-step kinetics of transcription initiation. R. Soc. Open Sci. 5: 181170. DOI: 10.1098/rsos.181170. https://royalsocietypublishing.org/doi/10.1098/rsos.181170
Simulations and models data: https://datadryad.org/stash/dataset/doi:10.5061/dryad.c7v943t
DATA SET 2. Related to: SMD Oliveira*, A Häkkinen*, J Lloyd-Price, H Tran, V Kandavalli, and AS Ribeiro (2016) Temperature-Dependent Model of Multi-Step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements. PLoS Comput Biol 12(10):e1005174. DOI:10.1371/journal.pcbi.1005174 *Equal contributions. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005174
Microscopy (single-cell RNA numbers time series, temperature changes):https://drive.google.com/file/d/1RdlTyVO342AZAKzDk9XhV8zZ-oQ75BML/view?usp=sharing
DATA SET 1. Related to: A-B Muthukrishnan, A Martikainen, R Neeli-Venkata, and AS Ribeiro (2014) In vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli cells. PLoS ONE 9(9): e109005. DOI: 10.1371/journal.pone.0109005. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0109005
Microscopy (single-cell RNA numbers time series, stress responses):https://drive.google.com/file/d/1j4ehUUBApREQ0ZAIDYGAjJLhg3UGw7-H/view?usp=sharing
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