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142 results for “Origin of replication”
Replication package of "The Chemical Origins of Plasma Contraction and Thermalization in CO2 Microwave Discharges" by A.W. van de Steeg et al.
<p>Title: The Chemical Origins of Plasma Contraction and Thermalization in CO2 Microwave Discharges<br> Authors: A.W. van de Steeg, L. Vialetto, A.F. Sovelas da Silva, P. Viegas, P. Diomede, M.C.M. van de Sanden, G.J. van Rooij<br> Journal: The Journal of Physical Chemistry Letters<br> Date: 2022-02-11<br> Description: <br> In this letter first Thomson scattering measurements in pure CO2 plasma were reported. The measurements show a thermalazation of electron temperature and gas temperature occurs with increasing pressure, coinciding with plasma contraction.<br> A 1D model is coupled with these measurements to elucidate the mechanisms behind both phenomena. Thus, it is revealed that associative ionization of radicals plays a crucial role. It connects thermal properties (gas temperature, heat and mass transport) with electon properties. <br> Access rights: Open<br> License: Creative Commons Attribution 4.0</p> <p><br> This replication package consists of the raw data used for the creation of each figure, ie measurement data, together with the python scripts used for data treatment.</p> <p>Most raw data is in the form of .spe files. The python library (by D.v.d. Bekerom) calibrate_fiber_pos is always used to read these camera images.</p> <p>The modelling data can be found separately in the publication of L. Vialetto (ref 20 in the Letter).<br> </p>
Source data for "Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing"
<p>Source data for "Regulation of replication origin licensing by ORC phosphorylation reveals a two-step mechanism for Mcm2-7 ring closing" </p> <p>The data is organized by Figure and associated Supp Figure(s). A README file is included in each figure folder to explain the files.</p> <p>(note: Data is included for Figs2-7 and SuppFigs 2-8. Fig.1 and SuppFig.1 did not have any associated data matrices, so there is no upload for them here). </p> <p>Briefly, the single molecule data is included in several different formats, all generated from single-molecule TIRF-microscopy video files using Matlab:</p> <p>Integrated trace files "traces" include integrated fluorescence intensity at individual DNA molecules over a 20 minute reaction.</p> <p>Background-corrected trace files normalize the integrated fluorescence intensity to a local-average background, as described in the Methods section of the paper-- these are used for EFRET calculations.</p> <p>"Intervals" files include the start, end time, and duration of protein-DNA interactions and were generated from the trace files and the raw videos using the Imscroll program (available at: https://github.com/gelles-brandeis/CoSMoS_Analysis).</p> <p>EFRET vectors are concatenated vectors of the EFRET vs time values of all protein-DNA interactions in the experiment-- these are used to generate EFRET heat maps. </p> <p>Matlab analysis scripts used in the paper are uploaded in a separate folder "ALA_scripts_used_final". Several of these scripts reference custom Matlab functions from the Gelles lab which are available here: https://github.com/gelles-brandeis/jganalyze and should be downloaded along with my attached scripts file. </p> <p>note: Raw single-molecule video files have not been uploaded here due to large sizes, but can be provided upon request. </p>
GC Skew and origin of replication-related plots for all Archaea genomes.
<p>We generated data and plots exhaustively for all Archaea complete genomes in the <a href="https://www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=2157">NCBI dataset </a>in April 2022.</p> <p>Plots and data available:</p> <p><strong>SkewI and GC Skew:</strong></p> <ul> <li> <p> <strong>SkewI</strong> and <strong>GC content</strong> of every archaeon complete genome.</p> </li> <li> <p><strong>Cumulative GC Skew plot</strong> of every complete genome, with <strong>an estimation of the origin and termination</strong> point in the sequence, <strong>obtained by analyzing the plot</strong></p> </li> <li> <p>The same results are available sorted by taxonomy (Euryarchaeota, Crenarchaeota, Thaumarchaeota) and SkewI values.</p> </li> </ul> <p> </p> <p><strong>Dot Plots:</strong></p> <ul> <li> <p><strong>Dot plots</strong> comparing two by two each of the ten genomes having the highest SkewI value for any given taxonomy. An <strong>estimation of the origin of replication</strong> based on the cumulative GC Skew is represented.</p> </li> <li> <p>Dot plots comparing two by two a genome of <strong>high SkewI </strong>with a genome of <strong>low SkewI</strong>.</p> </li> </ul> <p> </p> <p><strong>Clinker</strong>:</p> <ul> <li> <p><strong>Comparison of genes around origin/terminus of replication within a taxonomy</strong>. Results obtained by running <strong>Clinker</strong> on a portion of 20 000 nucleotides before and after the origin/terminus of replication of all genomes belonging to the taxonomy.</p> </li> </ul> <p> </p> <p><strong>Violin plots</strong>:</p> <ul> <li> <p>Visual representation of the repartition of SkewI and GC Skew in different taxonomies of archaea and selected bacteria.</p> </li> <li> <p>Similar plots for <strong>TA skew</strong>, <strong>cumulative skew per codon position</strong> and <strong>cumulative skew for non-coding regions.</strong></p> </li> </ul> <p> </p> <p>Please refer to the readme file for further information about the results and references.</p>
Data set for the article "Synchronous replication initiation of multiple origins"
<p>This data set contains the data of the submitted article "Synchronous replication initiation of multiple origins". The data was generated using simulations in python that are linked below. Experiments indicate that E. coli initiates DNA replication at multiple origins synchronously in fast growth conditions. We study by mathematical modelling under what conditions replication is initiated synchronously.</p>
Exploring Gender Bias in Remote Pair Programming among Software Engineering Students: The Twincode Original Study and First External Replication (datasets)
<p>This repository contains the datasets of the original experiment (University of Seville, December 2021) and its first external replication (University of California, Berkeley, May 2022) of the Twincode exploratory study on the effects of gender bias in remote pair programming among software engineering students.</p>
Replication package for "On the family origins of human capital formation: Evidence from donor children"
<p>The package contains the code necessary to reproduce the tables in Lundborg, Plug, Wurtz-Rasmussen (forthcoming) "On the family origins of human capital formation: Evidence from donor children", Review of Economic Studies. Detailed instructions are also given about accessing the raw data.</p>
Replication data for: Spatial and temporal origins of the La Perouse low oxygen pool: A combined Lagrangian statistical approach
<p>This dataset contains:</p> <p>a) <strong>NEP36 </strong>daily Model (NEMO) Output from 20130228 till 20131005 in NetCDF format,</p> <p>b) Moving Vessel Profiler (<strong>MVP</strong>) Survey data gathered onboard the R/V Falkor during August 2013 in ASCII .mat files,</p> <p>c) Files required to initialize and run Lagrangian Particle tracking model <strong>ARIANE </strong>i.e. one mesh_mask file in netCDF format and one text file containing initial positions based on the Eulerian grid of the sliced NEP36 model</p> <p>d) the output files from running the particle tracking model ARIANE in NetCDF format</p>
Replication package for "Solar Eclipses and the Origins of Critical Thinking and Complexity".
<p>This replication package accompanies Litina and Roca-Fernández. “Solar Eclipses and the Origins of Critical Thinking and Complexity”. The Economic Journal. (forthcoming)</p>
Data from: The ORFIUS complex regulates ORC2 localization at replication origins (Flow cytometry)
<p>In this work, we use bromodeoxyuridine (BrdU)/propidium iodide cell cycle flow cytometry profiling to demonstrate that treatment of ovarian cancer cell lines with gene specific siRNAs, shRNAs, or drugs leads to minimal or no cell cycle arrest which might otherwise influence observed phenotypes. All raw FCS files for flow cytometry data presented in Figures 4E, 6G, S3A, S4C, S5B, S5F, S8C, S8D, S8E, S9C, S10C, and S12B are available here.</p>
Replication package for the article "Who chooses fast-track programs in mathematics? The role of class origin, ethnicity, and gender among Norwegian lower-secondary students", submitted to European Societies.
<p>This file contains a replication package for the article "Who chooses fast-track programs in mathematics? The role of class origin, ethnicity, and gender among Norwegian lower-secondary students", submitted to European Societies</p> <p>****************************************************************************************************************************************<br> The analyses in this article are of secondary data from Norwegian state registers. We analyzed the data with concession from The Norwegian Data Protection Authority, and under the auspices of a confidentiality agreement with Statistics Norway. All direct identifiers were stripped from the file prior to analysis. Data were handled in such a way as to protect individual’s privacy and confidentiality. This included storing these data on a secure Research Computing server and requiring each researcher working with the data to sign a confidentiality affidavit. Other parties may not access the data because it would violate the concession given by The Norwegian Data Protection Authority, and the confidentiality agreement with Statistics Norway. This prevents us from uploading the data to a public repository. <br> Researchers may apply to get access to such data, and the procedure one needs to follow is described at Statistics Norway’s webpage: <br> https://www.ssb.no/en/data-til-forskning/utlan-av-data-til-forskere<br> </p>
Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing
<p><strong>Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing.</strong></p> <p>Zhang, Annie, Massachusetts Institute of Technology, ORCID: 0000-0003-3939-2585</p> <p>DOI: 10.5281/zenodo.7814499</p> <p>Primary publication DOI: <a href="https://doi.org/10.1073/pnas.2305556120">https://doi.org/10.1073/pnas.2305556120</a></p> <p> </p> <p><strong>Folder Structure</strong></p> <p> </p> <p>Source data are organized based on the parent figures from the main text (Figs 1-6). Source data from supplementary figures associated are placed within the associated parent figure folder. All figures, their associated parent figures, and the experiment names from which these figures are derived are summarized in the 'Summary.xlsx' file.</p> <p> </p> <p><strong>File Formats</strong></p> <p><strong> </strong></p> <p>1. Integrated trace files are saved as .dat files.</p> <p> </p> <p>- These trace files are obtained by integrating the fluorescence intensity contained within each DNA spot, or Area of Interest (AOI), over the range of the experimental time frame. They can be read and viewed in Matlab or the Matlab program imscroll, which is publicly available: <a href="https://github.com/gelles-brandeis/CoSMoS_Analysis">https://github.com/gelles-brandeis/CoSMoS_Analysis</a>.</p> <p> </p> <p>- Naming of files:</p> <p>The experiment name is specified at the beginning of the file name.</p> <p>The excitation and emission fields are specified using the following abbreviations.</p> <p>Gex: Green excited (Donor excited)</p> <p>Rex: Red excited (Acceptor excited)</p> <p>GexRex: Green and red excited (Donor and acceptor excited)</p> <p>Gem: Green emission (Donor emission)</p> <p>Rem: Red emission (Acceptor emission)</p> <p> </p> <p> </p> <p>To read the .dat integrated trace files in Matlab the user may type: </p> <p>>>[fn fp] = uigetfile</p> <p>% use the dialog box to mouse click on the appropriate *.dat file, then type:</p> <p>>>eval(['load ' [fp fn] ' -mat'])</p> <p>% This loads an aoifits structure array into the Matlab command environment</p> <p> </p> <p>The integrated trace data is stored in the aoifits.data matrix. A description of the columns is in the aoifits.dataDescription.</p> <p> </p> <p>The first five columns within aoifits.data are the most relevant to view fluorescence emission intensities at individual AOIs over time.</p> <p>Column 1: aoinumber</p> <p>Column 2: framenumber</p> <p>Column 3: amplitude (of fluorescence emission)</p> <p>Column 4: xcenter of the aoi</p> <p>Column 5: ycenter of the aoi</p> <p> </p> <p> </p> <p>2. Time Intervals are stored as excel spreadsheet (.xlsx) files.</p> <p> </p> <p>These files contain the AOI numbers used for analysis and frame numbers that correspond to specific events, such as protein arrival and departure events.</p> <p> </p> <p> </p> <p>3. For experiments with <em>E</em><sub>FRET</sub> analysis performed, <em>E</em><sub>FRET</sub> values are stored as .mat matrix files.</p> <p> </p> <p>Column 1: Time in seconds after protein colocalization with DNA</p> <p>Column 2: <em>E</em><sub>FRET </sub>values</p> <p>Column 3: AOI number</p> <p>Column 4: Frame number</p>
Replication package for "Macroevolutionary Origins of Comparative Development"
<p> Replication files of the paper "Macroevolutionary Origins of Comparative Development," by Riahi, Ideen A. 2023.</p> <p>The package contains two Stata do files, "Riahi_tables.do” and "Riahi_figures.do," which produce all tables and figures of the paper. Two Stata data files, "Riahi_data.dta" and "TM_shp.dta," an xlsx file "Riahi_codebook," which describes the variables included in "Riahi_data.dta," and two txt file, “Riahi_data.txt” and “TM_shp.txt,” which present the data in ASCII format.</p>
Replication package for "Macroevolutionary Origins of Comparative Development"
<p> </p> <p><strong> Replication files and instruction for "Macroevolutionary Origins of Comparative Development," by Riahi, Ideen A. 2023 </strong></p>
Data from: The ORFIUS complex regulates ORC2 localization at replication origins (Flow cytometry)
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Data from: Replicated origin of female biased adult sex ratio in introduced populations of the Trinidadian guppy (Poecilia reticulata).
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Data from: The replication of Frataxin gene is assured by activation of dormant origins in the presence of a GAA-repeat expansion
It is well known that DNA replication affects the stability of several trinucleotide repeats, but whether replication profiles of human loci carrying an expanded repeat differ from those of normal alleles is poorly understood in the endogenous context. We investigated this issue using cell lines from Friedreich's ataxia patients, homozygous for a GAA-repeat expansion in intron 1 of the Frataxin gene. By interphase, FISH we found that in comparison to the normal Frataxin sequence the replication of expanded alleles is slowed or delayed. According to molecular combing, origins never fired within the normal Frataxin allele. In contrast, in mutant alleles dormant origins are recruited within the gene, causing a switch of the prevalent fork direction through the expanded repeat. Furthermore, a global modification of the replication profile, involving origin choice and a differential distribution of unidirectional forks, was observed in the surrounding 850 kb region. These data provide a wide-view of the interplay of events occurring during replication of genes carrying an expanded repeat.
Data from: Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins
Chromosomal DNA elements are organized into spatial domains within the eukaryotic nucleus. For example, sites actively undergoing DNA replication, high-level transcription, and repair of double-strand breaks coalesce into foci, although the significance and mechanisms giving rise to these dynamic structures are poorly understood. In S. cerevisiae, replication origins exhibit characteristic subnuclear localizations prior to S phase that anticipate their initiation timing and/or efficiency during S phase: origins found within the nuclear interior in G1 phase initiate early and efficiently in S phase while origins found associated with the nuclear periphery in G1 phase initiate later and less efficiently. In this study, we link interior localization of replication origins in G1 phase with Fkh1 activity, which is required for their early replication timing. Using a Fkh1-dependent origin relocalization assay, we determine that execution of Dbf4-dependent kinase function, including Cdc45 loading, results in dynamic relocalization of a replication origin from the nuclear periphery to the interior in G1 phase. Origin mobility increases substantially with Fkh1-driven relocalization. These findings provide novel molecular insight into the mechanisms that govern dynamics and spatial organization of DNA replication origins and possibly other functional DNA elements.
A Meritocratic Origin of Egalitarian Behavior - Replication package
<p>Replication package</p>
Data from: Dynamic relocalization of replication origins by Fkh1 requires execution of DDK function and Cdc45 loading at origins
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Data from: The replication of Frataxin gene is assured by activation of dormant origins in the presence of a GAA-repeat expansion
Open the record for dataset details and reuse information.
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