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ShareScore release 0.9.0
Dataset results
11 results for “protein-DNA interactions”
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>
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
GEO Series GSE13047. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Paired Imaging and Sequencing of Protein-DNA Interactions in Single Human Cells Using microDamID
GEO Series GSE156150. Homo sapiens. 74 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type specific profiling of protein-DNA interactions in Drosophila melanogaster
GEO Series GSE159632. Drosophila melanogaster. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
An ancient protein-DNA interaction underlying metazoan sex determination
GEO Series GSE64892. Homo sapiens; Mus musculus. 7 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells
GEO Series GSE299567. Mus musculus; Homo sapiens. 17 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Protocol for Mapping Protein-DNA Interactions with Directed Methylation with Long-read Sequecing (DiMeLo-seq)
GEO Series GSE208125. Homo sapiens; Drosophila melanogaster. 4 samples. Type: Other.
ChEC-Seq: a robust method to identify protein-DNA interactions genome-wide
GEO Series GSE133645. Saccharomyces cerevisiae. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells
GEO Series GSE103125. Homo sapiens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide protein-DNA interaction analysis of CceR and AkgR transcription factors
GEO Series GSE63449. Cereibacter sphaeroides. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Calling Cards: a customizable platform to longitudinally record protein-DNA interactions over time in cells and tissues
GEO Series GSE223926. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.