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662 results for “RNA Polymerase II”
Dataset 2. Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II
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Analysis of RNA polymerase II clusters in fixed embryos injected with antigen-binding fragments
<p>Data and scripts for the analysis of RNA polymerase II clusters. The data set includes data obtained from fixed zebrafish embryos injected with antigen-binding fragments, CellProfiler pipelines for the initial analysis of images are provided, along with Python scripts to export data into CSV format and execute downstream analysis.</p>
Analysis of RNA polymerase II phosphorylation in two-color STED microscopy images
<p>This data set includes the raw image data and MatLab analysis scripts to assess the relative distribution of RNA polymerase II C-terminal domain serine 5 and serine 2 phosphorylation in zebrafish embryos. Phosphorylated polymerase II was labeled by immunofluorescence, microscopy images were acquired by STED microscopy and analyzed using MatLab scripts. This extended version now contains image data and analysis scripts to two alternative sets of antibodies.</p>
Example micrographs of RNA polymerase II localization to the zebrafish microRNA miR-430 cluster
<p>Contains the raw images and MatLab scripts to show localization of recruited (Ser5P) and elongating (Ser2P) RNA polymerase II to the zebrafish microRNA miR-430 cluster. Embryos were fixed in the oblong stage of development, labeled by immunofluorescence, and images were recorded with an instant-SIM microscope.</p> <p>To produce example images, first run the extraction script, then the example images script. You need to add the bfmatlab importer function from OME for data import before running the extraction script. Otherwise, extracted data are also provided with this repository,</p>
Analysis of antibody signal loss for elongating RNA polymerase II upon transcription inhibition
<p>This data set assesses the loss of antibody signal for elongating RNA polymerase II in zebrafish embryos upon transcription inhibition with flavopiridol. Polymerase was labeled by immunofluorescence, microscopy images were acquired by instant-SIM micrscopy, and analyzed using MatLab scripts and the bioformats importer. This data set contains the raw image data as well as all further analysis scripts.</p>
Microscopy images of the DNA and RNA polymerase II distribution inside nuclei of cell cultures obtained from pluripotent zebrafish embryos
<p><strong>Image data description</strong></p> <p>Color channels in the image data:</p> <ol> <li>First channel: DNA (Hoechst 33342)</li> <li>Second channel: Pol II Ser2P (Elongating RNA polymerase II, indirect immunofluorescence, STAR RED)</li> <li>Third channel: Pol II Ser5P (Recruited RNA polymerase II, indirect immunofluorescence, Alexa 594)</li> </ol> <p><strong>Sample description</strong></p> <p>Praimary cell cultures were prepared from pluripotent zebrafish embryos were collected at the sphere stage of development, treated with chemical inhibitors of transcription (Control, 500 mM Flavopiridol, 500 mM Triptolide, all for 30 min) and fixed overnight (2% formaldehyde in culutre media, 30 min, room temperature; followed by 8% formaldehyde for 15 min at room temperature). RNA polymerase in the recruited state (Pol II Ser5P) and the elongating state (Pol II Ser2P) were labeled by indirect immunofluorescence (permeabilization 0.5% Triton X-100 in PBS 15 min room temperature, 30 min blocking 4% BSA in PBST, rat IgG anti-Pol II Ser5P & rabbit IgG anti-Pol II Ser2P in 4% BSA in PBST overnight 4°C, anti-rat Alexa 594 & anti-rabbit STAR RED in 4% BSA in PBST overnight 4°C). Mounted in VectaShield H-1000 with 2 µM Hoechst 33342 added for fluorescent DNA labeling. Scan of lab book page is included in the repository.</p> <p>The data set contains images obtained from two samples for each condition.</p> <p><strong>Imaging</strong></p> <p>Microscopy images acquired using VisiTech iSIM with dual camera setup. Objective Nikon CFI SR HP Apo<br> TIRF 100XAC Oil, color channels acquired in a sequence to reduce overlap (DNA + Ser2P acquired simultaneously on two camerase, Ser5P acquired after on a single camera), z-stack settings optimized to ensure reliable xyz alignment of channels. Imags were cropped to the region with best signal and resolution in the DNA channel, same region used throughout the entire dataset. all imaging settings were kept unchanged over the course of acquisition, all images acquired in a single session of 4 hours.</p> <p><strong>Advice for image processing</strong></p> <p>Images can be loaded for processing with the OME bioformats importer. An import script for MatLab is available through the Hilbert lab: https://github.com/lhilbert/NuclearObjects_ImageAnalysis</p> <p><strong>Author contributions</strong></p> <p>AN & MS provided embryos, carried out cell culture, and prepared samples, LH performed microscopy</p>
Microscopy data (1/2): interaction of the gene iscub with RNA polymerase II clusters in inhibitor-treated zebrafish embryos
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>iscub</em> and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names.</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data (2/3): interaction of the gene foxd5 with RNA polymerase II clusters in inhibitor-treated zebrafish embryos
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>foxd5</em> and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names.</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data (3/3): interaction of the gene foxd5 with RNA polymerase II clusters in inhibitor-treated zebrafish embryos
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>foxd5</em> and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names.</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data (1/3): interaction of the gene foxd5 with RNA polymerase II clusters in inhibitor-treated zebrafish embryos
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>foxd5</em> and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names.</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data (2/2): interaction of the gene iscub with RNA polymerase II clusters in inhibitor-treated zebrafish embryos
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>iscub</em> and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated for 30 minutes prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names.</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy-based assessment of H3K27-acetylation at RNA polymerase II clusters during early stages of zebrafish embryo development
<p>This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Marcel Sobucki in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert.</p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>Additional data needed to be stored in an extra repository due to size limitations: <a href="https://doi.org/10.5281/zenodo.8028508">https://doi.org/10.5281/zenodo.8028508</a></p>
Microscopy-based assessment of RNA polymerase II clusters in zebrafish embryos treated with JQ1 and flavopiridol (additional data)
<p>This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters in zebrafish embryos treated with the inhibitors JQ1 or flavopiridol. Samples were prepared and images were recorded by Süheyla Eroglu-Kayikci and Elisa Kämmer in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert.</p> <p>This repository contains additional data to the following main repository: <a href="https://doi.org/10.5281/zenodo.8019764">https://doi.org/10.5281/zenodo.8019764</a></p>
Microscopy-based assessment of RNA polymerase II clusters in zebrafish embryos treated with JQ1 and flavopiridol
<p>This repository contains the data and MatLab analysis scripts of the analysis of histone 3 lysine 27 acetylation (H3K27ac) at RNA polymerase II clusters in zebrafish embryos treated with the inhibitors JQ1 or flavopiridol. Samples were prepared and images were recorded by Süheyla Eroglu-Kayikci and Elisa Kämmer in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert.</p> <p>To analyse date data, the raw image data are first extracted into MatLab-native files using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/MultiPosition_extraction_nd2.m">MultiPosition_extraction_nd2.m</a> script. The actual analysis is then carried out using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ClusterAnalysis.m">ClusterAnalysis.m</a> script. Example microscopy images were produced using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ExampleImages.m">ExampleImages.m</a> script. The extracted data can be reviewed using the <a href="https://zenodo.org/api/files/2f2192f4-a05c-4969-ba0a-4f235b837709/ReviewExtractedStacks.m">ReviewExtractedStacks.m</a> script.</p> <p>Additional data, stored in separate repository due to size limits: <a href="https://doi.org/10.5281/zenodo.8023349">https://doi.org/10.5281/zenodo.8023349</a></p>
Translin facilitates RNA polymerase II dissociation and suppresses genome instability during RNase H2- and Dicer-deficiency (data files)
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Data from: A global change in RNA polymerase II pausing during the Drosophila midblastula transition
Massive zygotic transcription begins in many organisms during the midblastula transition when the cell cycle of the dividing egg slows down. A few genes are transcribed before this stage but how this differential activation is accomplished is still an open question. We have performed ChIP-seq experiments on tightly staged Drosophila embryos and show that massive recruitment of RNA polymerase II (Pol II) with widespread pausing occurs de novo during the midblastula transition. However, ∼100 genes are strongly occupied by Pol II before this timepoint and most of them do not show Pol II pausing, consistent with a requirement for rapid transcription during the fast nuclear cycles. This global change in Pol II pausing correlates with distinct core promoter elements and associates a TATA-enriched promoter with the rapid early transcription. This suggests that promoters are differentially used during the zygotic genome activation, presumably because they have distinct dynamic properties.
Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation (Supplementary Tables)
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RNA polymerase I, II, and III metamap
<p>Processed files related to our manuscript: Rajendra K C et al., <em>Evidence of RNA polymerase III recruitment and transcription at protein-coding gene promoters</em></p> <p> </p>
Microscopy data: interaction of the gene zgc::64022 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>zgc::64022</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, between one and three samples were prepared per stage and experiment (001, 002 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
Microscopy data: interaction of the gene vamp2 with RNA polymerase II clusters during early zebrafish embryo development
<p>Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II.</p> <p>This data set is for the gene <em>vamp2</em> and is obtained from fixed zebrafish embryos, collected at the developmental stages oblong, sphere, dome, 30% epiboly, and 50% epiboly (indicated in the file names). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two independent experiments were performed (IF1, IF2 in the file name), for each experiment, between one and three samples were prepared per stage and experiment (001, 002, 003 in the file name).</p> <p>The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).</p>
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