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Dataset results
157 results for “DNA Polymerase”
RNA Polymerase-II-generated DNA supercoils destabilize nucleosomes
GEO Series GSE47795. Drosophila melanogaster. 25 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [miRNA-seq]
GEO Series GSE203325. Arabidopsis thaliana. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
The second subunit of DNA-polymerase delta is required for genomic stability and epigenetic regulation
GEO Series GSE79259. Arabidopsis thaliana. 18 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
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.
Exploring the Respective Contributions of DNA Polymerase Proofreading and Mismatch Repair in the Shaping of Spontaneous Mutation Rates.
GEO Series GSE239804. Bacillus subtilis subsp. subtilis str. 168. 12 samples. Type: Expression profiling by high throughput sequencing.
Co-targeting RNA Polymerases IV and V promotes efficient de novo DNA methylation in Arabidopsis
GEO Series GSE124546. Arabidopsis thaliana. 246 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Figure 1 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 1 Graptopetalum paraguayense E. Walther.
Figure 4 from: Todorova N, Rangelov M, Dincheva I, Badjakov I, Enchev V, Markova N (2022) Potential of hydroxybenzoic acids from Graptopetalum paraguayense for inhibiting of herpes simplex virus DNA polymerase – metabolome profiling, molecular docking and quantum-chemical analysis. Pharmacia 69(1): 113-123. https://doi.org/10.3897/pharmacia.69.e79467
Figure 4 Fitting of phenolic acids in the DNA polymerase pocket.
The dynamic interaction between DNA polymerase beta and eta with an RNA-DNA hybrid
<p>The videos have shown that DNA polymerase beta (5TBB) exhibited dynamic interaction with a 1 nt-gap substrate containing an RNA template through the formation of base-pairing between the incoming nucleotide with the RNA template base. In contrast, DNA polymerase eta (4J9N) exhibited dynamic interaction with an open RNA template with disrupted base-pairing.</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>
Detection of Chlamydia DNA by Polymerase Chain Reaction in Primary Tubal and Ovarian Cancers Tissues : a Pilot Study
ClinicalTrials.gov study NCT02343510. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diagnosis and Treatment of Urinary Tract Infection Using DNA Polymerase Chain Reaction Versus Urine Culture
ClinicalTrials.gov study NCT06808451. IPD Sharing: NO. Countries: 1. Publications: 0.
FVE promotes RNA-directed DNA methylation by facilitating the association of RNA polymerase V with chromatin [RNA-seq]
GEO Series GSE169174. Arabidopsis thaliana. 14 samples. Type: Expression profiling by high throughput sequencing.
Mitochondrial Polymerase Gamma Dysfunction and Aging Cause Cardiac Nuclear DNA Methylation Changes [100929_MM9_Deluxe_Prom_Meth_HX1]
GEO Series GSE72889. Mus musculus. 16 samples. Type: Methylation profiling by genome tiling array.
Activity of DNA polymerase kappa across the genome in human fibroblasts
GEO Series GSE260451. Homo sapiens. 18 samples. Type: Other.
Comparison of the transcriptome of DNA polymerase zeta deficient and proficient mouse embryonic fibroblasts.
GEO Series GSE163313. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Control of RNA polymerase II promoter-proximal pausing by DNA supercoiling [ChIP-seq]
GEO Series GSE141798. Homo sapiens. 16 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
An siRNA-guided AGO protein recruits Polymerase V to initiate RNA-directed DNA methylation
GEO Series GSE165575. Arabidopsis thaliana. 111 samples. Type: Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
An siRNA-guided AGO protein recruits Polymerase V to initiate RNA-directed DNA methylation (BSA-seq dataset)
GEO Series GSE165573. Arabidopsis thaliana. 66 samples. Type: Methylation profiling by high throughput sequencing.
Mithramycin Alters EWS::FLI1 DNA Binding and RNA Polymerase II Processivity to Inhibit Nascent Transcription [RNA-seq]
GEO Series GSE316978. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
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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.