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37 results for “Origins of DNA replication”
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>
Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation
GEO Series GSE186675. Homo sapiens. 5 samples. Type: Other.
High-Resolution Profiling of Drosophila Replication Start Sites Reveals a DNA Shape and Chromatin Signature of Metazoan Origins
GEO Series GSE65692. Drosophila melanogaster. 9 samples. Type: Other.
Mapping origins of replication in Arabidopsis thaliana: Examination of BrdU labeled DNA and unlabeled DNA in one cell type
GEO Series GSE21781. Arabidopsis thaliana. 4 samples. Type: Other.
Eukaryotic origin-dependent DNA replication in vitro reveals sequential action of DDK and S-CDK kinases.
GEO Series GSE29646. Saccharomyces cerevisiae. 4 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome
GEO Series GSE61743. Saccharomyces cerevisiae. 8 samples. Type: Genome binding/occupancy profiling by genome tiling array.
HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors
GEO Series GSE57619. Saccharomyces cerevisiae W303; Saccharomyces cerevisiae. 52 samples. Type: Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing.
KMT2C/KMT2D-dependent H3K4me1 mediates DNA replication timing and origin firing
GEO Series GSE277790. Mus musculus. 12 samples. Type: Other.
High resolution mapping of DNA replication origins in human genome
GEO Series GSE10217. Homo sapiens. 4 samples. Type: Other.
HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors [Mnase-seq]
GEO Series GSE57618. Saccharomyces cerevisiae. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans.
GEO Series GSE140804. Caenorhabditis elegans. 63 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins
GEO Series GSE131699. Mus musculus. 7 samples. Type: Other.
A predictable conserved DNA base composition signature defines human core DNA replication origins
GEO Series GSE128477. Homo sapiens. 44 samples. Type: Other; Expression profiling by high throughput sequencing.
Allele-Specific Analysis of DNA Replication Origins in Mammalian Cells
GEO Series GSE61972. Homo sapiens. 1 samples. Type: Other.
RECQL4 is not critical for firing of human DNA replication origins
GEO Series GSE225532. Homo sapiens. 31 samples. Type: Other.
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency
GEO Series GSE220757. Saccharomyces cerevisiae. 6 samples. Type: Other.
Genome-wide mapping of human DNA-replication origins: levels of transcription at Orc1 sites regulate origin selection and replication timing
GEO Series GSE37583. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
GEO Series GSE118484. Drosophila melanogaster. 58 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
HDACs act on ribosomal DNA to control the yeast replication program and the competition between origins for limiting initiation factors [ChIP-seq]
GEO Series GSE57617. Saccharomyces cerevisiae. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
JQ1 prevents BRD4 recruitment to the lytic origins of replication [Akata-Zta DNA-seq]
GEO Series GSE98772. Homo sapiens; human gammaherpesvirus 4. 8 samples. Type: Other.
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