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38 results for “DNA probe”
Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies
<p>Data corresponding to the paper "Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies."<br> <br> Corresponding scripts can be found at: <a href="https://github.com/pjhop/dnamarray_crossreactivity">https://github.com/pjhop/dnamarray_crossreactivity</a><br> All downstream analyses in <a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/c9_analysis.Rmd">c9_analysis.Rmd</a> and in<a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/supplementary_note.Rmd"> supplementary_note.Rmd</a> can be reproduced using the deposited data as follows:</p> <ul> <li>Clone the dnamarray_crossreactivity repository: < git clone https://github.com/pjhop/dnamarray_crossreactivity.git ></li> <li>Download the data ('data.zip') and place it in the 'dnamarray_crossreactivity' folder.</li> <li>Unzip the data.zip folder</li> </ul> <p>Scripts used to generate the data in each subdirectory can be found at:</p> <ul> <li>data/processed/c9_matches/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches</a></li> <li>data/output/ewas/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas</a></li> <li>data/output/figs/: empty folder, running 'c9_analysis.Rmd' will save figures here.</li> <li>data/misc/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other</a></li> <li>data/extdata: <ul> <li>Zhou <em>et al.</em> annotations (EPIC.hg19.manifest.tsv.gz, HM450.hg19.manifest.pop.tsv.gz, HM450.hg19.manifest.tsv.gz) were downloaded from: <a href="https://zwdzwd.github.io/InfiniumAnnotation">https://zwdzwd.github.io/InfiniumAnnotation</a> (downloaded at 17/09/2020)</li> <li>Naeem <em>et al.</em><em> </em>data (12864_2013_7006_MOESM2_ESM.csv) was downloaded from: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/</a></li> <li>Chen <em>et al.</em> data (48639-non-specific-probes-Illumina450k.xlsx) was downloaded from <a href="https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx">https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx</a></li> <li>The anno_450k.txt.gz and anno_EPIC.txt.gz are subsets of the annotation files included in the following package respectively: <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html</a> and <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html</a></li> </ul> </li> <li> data/genome_bs: Scripts used to generate these data can be found at <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R</a> and <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R</a> .</li> <li> data/raw: Individual-level data is available upon access at: <a href="https://ega-archive.org/studies/EGAS00001004587">https://ega-archive.org/studies/EGAS00001004587</a></li> </ul>
NMR titration experiments that study binding of a NIR emitting osmium polypyridyl probe to cMYC and hTel G-quadruplex DNA
<p>1D and 2D NMR spectra of cMYC and hTel G-quadruplex DNA and their complexes with Λ-<strong> </strong>and Δ<strong>-</strong>enantiomers of the osmium polypyridyl probe [Os(TAP)<sub>2</sub>(dppz)]<sup>2+</sup>. Spectra were recorded on a 600 MHz NMR spectrometer with 70 mM KCl, 20 or 25 mM K-phosphate buffer, pH 7, 298 K, in 90% H<sub>2</sub>O and 10% D<sub>2</sub>O at 25 °C.</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4e
<p>The single-molecule FRET dataset underlying Fig. 4e of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4f
<p>The single-molecule FRET dataset underlying Fig. 4f of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage - Fig. 4d
<p>The single-molecule FRET dataset underlying Fig. 4d of "A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage", DOI: 10.1039/C8SC00681D</p>
FIGURE 1 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 1 | Characidium sp. aff. C. vidali karyotypes arranged from mitotic metaphases after to conventional Giemsa staining and C-banding. A. and C. male karyotypes. B. and D. female karyotypes. B chromosomes are in the boxes. In evidence a preserved specimen under study. Photo of Characidium sp. aff. C. vidali by Bruno F. Melo.
FIGURE 3 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 3 | Metaphase plates of Characidium sp. aff. C. vidali after fluorescent in situ hybridization (FISH) with four microsatellite motifs. B chromosomes present in the species are indicated. Scale bar = 10 µm.
FIGURE 2 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 2 | Metaphase of Characidium sp. aff. C. vidali after FISH with histone H3 (green) and H4 (red) probe. Synteny marked in par 10. Scale bar = 10 µm.
FIGURE 4 in Cytomolecular investigations using repetitive DNA probes contribute to the identification and characterization of Characidium sp. aff. C. vidali (Teleostei: Characiformes)
FIGURE 4 | Metaphase of Characidium sp. aff. C. vidali after fluorescent in situ hybridization (FISH); A. With a telomeric probe (TTAGGG) n. B. After sequential C-banding. The arrows indicate Interstitial Telomeric Sites (ITS), and asterisks highlight double-ITS marks; B = B-chromosomes; Z, W = sex chromosomes. Scale bars = 10 µm.
SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing
<p>Studies of in vivo chromatin organization have relied on the accessibility of the underlying DNA to nucleases or methyltransferases, which is limited by their requirement for purified nuclei and enzymatic treatment. Here, we introduce a nanopore-based sequencing technique called Small-Molecule Adduct sequencing (SMAdd-seq), where we profile chromatin accessibility by treating nuclei or intact cells with a small molecule, angelicin. Angelicin reacts with thymine bases in linker DNA not bound to core nucleosomes after UV light exposure, thereby labeling accessible DNA regions. By applying SMAdd-seq in Saccharomyces cerevisiae, we demonstrate that angelicin-modified DNA can be detected by its distinct nanopore current signals. To systematically identify angelicin modifications and analyze chromatin structure, we developed a neural network model, NEural network for mapping MOdifications in nanopore long-reads (NEMO). NEMO accurately called expected nucleosome occupancy patterns near transcription start sites at both bulk and single-molecule levels. We observe heterogeneity in chromatin structure and identify clusters of single-molecule reads with varying configurations at specific yeast loci. Furthermore, SMAdd-seq performs equivalently on purified yeast nuclei and intact cells, indicating the promise of this method for in vivo chromatin labeling on long single molecules to measure native chromatin dynamics and heterogeneity.</p>
Targeted DNA methylation from cell free DNA using hybrid probe capture
<p>CSV files contain beta value and coverage per base & per region, as indicated in the file name.<br> Columns are samples, rows are CpGs or target region - depending on the file.</p> <p>Files were generated from our bismark/bsseq pipeline as described in the manuscript.</p> <p>Contact: dnbuckle@usc.edu</p>
Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices
<p>Readme.txt, 16.07.2021<br> Fontana et al.<br> “Probing DNA - transcription factor interactions using single-molecule fluorescence detection in nanofluidic devices”</p> <p>pre-print: https://doi.org/10.1101/2021.05.12.443786 (BioRxiv)</p> <p>The repository contains the raw data ("*.tif") files, data from subsequent analysis steps performed in Matlab ("*.mat") and obtained histograms.</p> <p>For further information, please contact<br> dr. Johannes Hohlbein @ Wageningen University & Research<br> (johannes.hohlbein@wur.nl)</p>
Data from: Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaints probes enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses only molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence. We used three-dimensional stochastic optical reconstruction microscopy (3D-STORM) and optimized the imaging conditions to efficiently distinguish sparsely distributed Alexa-647 from background cellular autofluorescence. Utilizing 3D-STORM and 29-34 individual MB probes, we observed 3D fine-scale nanostructures of 2.5 kb integrated or endogenous unique DNA in situ in the human or mouse genome, respectively, demonstrating the capability of MB-based FISH in visualizing a so far shortest and non-repetitive genomic sequence in 3D at super-resolution.
Effect of Microhydration in Tuning the Photophysical Behavior of a Luminescent DNA Probe Revealed by Non-Adiabatic Dynamics: Geometries
<p>Starting geometries for the 50 computed trajectories. These geometries come from a Wigner distribution around the minimum geometry of the ground state.</p>
Supplementary material 4 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
COI library ASV tax
Supplementary material 1 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
File S1
Supplementary material 3 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
16S library ASV tax
Supplementary material 5 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Unassigned COIASVs krona
Supplementary material 2 from: Hintikka S, Carlsson JE, Carlsson J (2022) The bacterial hitchhiker's guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. Metabarcoding and Metagenomics 6: e80416. https://doi.org/10.3897/mbmg.6.80416
Metadata all
G-Quartets, 4-Way Junctions and Triple Helices but not DNA Duplexes: Planarization of Twisted Push-Pull Flipper Probes by Surface Recognition Rather than Physical Compression
<p>Original fluorescence data and corresponding notebook pages</p>
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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)
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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.