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662
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ShareScore release 0.9.0
Dataset results
662 results for “RNA Polymerase II”
G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [RNA-seq]
GEO Series GSE169465. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Integrative analysis of RNA Polymerase II and transcriptional dynamics upon Myc activation [RNA-seq]
GEO Series GSE98418. Mus musculus. 66 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide profiling of PPARγ:RXR and RNA polymerase II
GEO Series GSE13511. Mus musculus. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and controls RNA polymerase pause release at select gene targets [ChIP-Seq II]
GEO Series GSE206815. Homo sapiens. 18 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
CDK12 maintains phosphorylation of RNA Polymerase II during epidermal differentiation
GEO Series GSE166407. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA Polymerase II- and III-mediated expression
GEO Series GSE106976. Mus musculus. 21 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
The Cdk8 kinase module regulates Mediator-RNA polymerase II interaction
GEO Series GSE161140. Saccharomyces cerevisiae. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA polymerase II is necessary for spatial chromatin reorganization following exit from mitosis [RNA-Seq]
GEO Series GSE176285. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Association with Aurora-A controls N-MYC-dependent promoter escape and pause release of RNA polymerase II during the cell cycle
GEO Series GSE78957. Homo sapiens. 50 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Co-transcriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
GEO Series GSE56279. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Cdk11-Cyclin L controls the assembly of the RNA polymerase II Mediator [expression]
GEO Series GSE37960. Schizosaccharomyces pombe. 8 samples. Type: Expression profiling by array.
RNA polymerase II CTD S2P is dispensable during embryogenesis but regulates the developmental diapause in C. elegans [RNA-seq]
GEO Series GSE145457. Caenorhabditis elegans. 16 samples. Type: Expression profiling by high throughput sequencing.
Epigenome mapping in quiescent cells reveals a key role for H3K4me3 in regulation of RNA polymerase II activity
GEO Series GSE280066. Schizosaccharomyces pombe. 50 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A role for the RNA Polymerase II-CTD phosphatase, FCP1 in the oxidative stress response
GEO Series GSE128936. Saccharomyces cerevisiae. 16 samples. Type: Expression profiling by array.
Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster [ChIPseq-PolII-S5]
GEO Series GSE116886. Drosophila melanogaster. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Dataset of live imaging of RNA Polymerase II CTD phosphorylation in zebrafish embryos
<p>Images are recruited RNA polymerase II Serine 5 (Pol II Ser5P) and RNA polymerase II Serine 2 (Pol II Ser2P) in live sphere stage zebrafish embryos, visualized with antibody fragments (Fab) labelled with Janelia Fluor 647 and Alexa Fluor 488, respectively.<br> <br> Dataset "<strong>EmbryoC_20ms_040.nd2" </strong>is recorded by 20 ms exposure time and contains 120 frames. Dataset "<strong>EmbryoC_50ms_042.nd2</strong>" contains images recorded with 50 ms exposure time and contains 61 frames. </p>
Microscopy-based analysis of the DNA and RNA polymerase II distribution inside nuclei of 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>Pluripotent zebrafish embryos were collected at the sphere stage of development and fixed overnight (0.3X Danieu's media with 2% formaldehyde, 0.2% Tween-20, 4°C). RNA polymerase in the recruited form (Pol II Ser5P) and the elongating form (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:</p> <ul> <li>One sample (8 embryos in the sample) with all three colors labeled (Main Sample)</li> <li>One sample (3 embryos) in which the primary antibodies were omitted to allow assessment of cross-talk to the DNA channel (No Primary Antibodies)</li> <li>One sample (1 embryo) in which no Hoechst was added to the mounting media to allows assessment of cross-talk to the immunofluorescence channels (No Hoechst)</li> </ul> <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>Image analysis scripts</strong></p> <p>Scripts for the image analysis of the shapes of Pol II clusters in relation to transcription levels are provided as MatLab files. The MatLab script MultiPosition_extraction.m should be run as the first script, and requires that the bfmatlab toolbox from the Open Microscopy Environment is installed and added to the path permanently. Then, the script ReviewExtractedStacks.m was used to sort out images from the image folder that are clearly dominated by prominent miR-430 foci. Following this, the script AmphiphileExampleImages.m can be used to produce example images, and the script ClusterAnalysis_Amphiphile.m to carry out the actual image analyses. A figure prepared from the final image analysis is also provided for guidance.</p> <p><strong>Author contributions</strong></p> <p>AN & MS provided embryos and prepared samples, LH performed microscopy</p>
Microscopy-based assessment of RNA polymerase II clusters during sperm precursor formation in fruit fly testes
<p>This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of differentiation into sperm precursor cells in fruit fly testes. Fruit flies were raised in Sylvia Erhardt's laboratory, samples prepared and microscopy images recorded by Agnieszka Pancholi, and images analysed 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>
Neurological Cockayne Syndrome Results from R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation
GEO Series GSE226204. Homo sapiens; Mus musculus. 37 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
A gene-specific requirement of RNA polymerase II CTD phosphorylation on serine 2 for sexual differentiation in fission yeast
GEO Series GSE16498. Schizosaccharomyces pombe. 29 samples. Type: Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array.
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OpenNeuro
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