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148 results for “DNA accessibility”
Fig. 1 in Callicultureinducingfromredclover(Trifolium Pratense L.) Wild Accessions And Results Of Dna Extraction
Fig. 1. Results of flow cytometry: a) 2n ploidy control, b) the typical result for leaves, c) the typical result for stems, d) the typical result for roots.
Index and biological spectrum of accessible DNA elements in the human genome
<p>Data associated with the manuscript titled<br> "Index and biological spectrum of accessible DNA elements in the human genome"<br> <a href="https://doi.org/10.1101/822510">https://doi.org/10.1101/822510</a></p> <p>Code repositories for these data are available here:</p> <ul> <li>https://github.com/Altius/Index</li> <li>https://github.com/Altius/Vocabulary</li> </ul> <p><br> Tab-separated file with DNase I Hypersensitive Site (DHS) coordinates,<br> including DHS summits and core regions and assignments to regulatory components.<br> A separate legend file describes the contents of each column in more detail.</p> <ul> <li>DHS_Index_and_Vocabulary_hg38_WM20190703.txt.gz</li> <li>DHS_Index_and_Vocabulary_hg19_WM20190703.txt.gz (mapped using liftOver, not ideal)</li> <li>DHS_Index_and_Vocabulary_legend.txt</li> </ul> <p> </p> <p>Metadata files describing biosample characteristics and annotations,<br> provided in HTML, PDF, TSV and Excel formats:</p> <ul> <li>DHS_Index_and_Vocabulary_metadata.html</li> <li>DHS_Index_and_Vocabulary_metadata.pdf</li> <li>DHS_Index_and_Vocabulary_metadata.tsv</li> <li>DHS_Index_and_Vocabulary_metadata.xlsx</li> </ul> <p> </p> <p>Presence/absence matrix of DHSs (rows) versus biosamples (columns),<br> provided in RData, MatrixMarket and raw formats:</p> <ul> <li>dat_bin_FDR01_hg38.RData</li> <li>dat_bin_FDR01_hg38.mtx.gz</li> <li>dat_bin_FDR01_hg38.txt.gz</li> <li>dat_bin_FDR01_hg19.RData (mapped using liftOver, not ideal)</li> <li>dat_bin_FDR01_hg19.txt.gz (mapped using liftOver, not ideal)</li> </ul> <p> </p> <p>Normalized DNase-seq signal matrix of DHSs (rows) versus biosamples (columns),<br> provided in RData and raw formats:</p> <ul> <li>dat_FDR01_hg38.RData</li> <li>dat_FDR01_hg38.txt.gz</li> </ul> <p>The order of DHSs (rows) is the same as in the DHS Index file(s) above,<br> and the order of biosamples (columns) is the same as in the metadata files.</p> <p> </p> <p>Non-negative Matrix Factorization (NMF) results, decomposing the presence/absence matrix (hg38) into 16 components:</p> <ul> <li>2018-06-08NC16_NNDSVD_Mixture.npy.gz</li> <li>2018-06-08NC16_NNDSVD_Basis.npy.gz</li> </ul> <p> </p> <p>Putative transcription factor-specific regulatory elements,<br> identified using DHS Vocabulary components, TF motif databases and biosample-specific footprinting data:</p> <ul> <li>TF_associated_DHSs_hg38.tar.gz</li> </ul>
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>
Quantitation of human sperm DNA accessibility and DNA nicking by NicE-view and Nick translation imaging
<ul> <li>Accessible or nicked DNA from human sperm was labelled using NicE-view, ATAC-See or nick translation.</li> <li>For nick translation and NicE-view 60 individuals were profiled, for 57 of these individuals two samples were available (1 for total sperm and 1 for sperm selected for motility via the swim-up method), while for the final 3 only total sperm was available (filename: Gill_NicE_view_CellProfiler.csv).</li> <li>For ATAC-See data from 5 individuals were generated (Gill_ATAC_See_CellProfiler.csv).</li> <li>For a further 6 individuals sperm were isolated by FACS following labelling with the DNA dye CMA3 and subjected to T4 NicE-view (Gill_NicE_view_CMA3_Cell_Profiler.csv).</li> <li>Finally a data set containing double labelling of DNA nicks and DNA accessibility was generated for 6 individuals (Gill NicE_view_Double_Labelling_CellProfiler.csv).</li> <li>For each sample 400 Z-projections were generated and quantified using CellProfiler. Data are saved in .csv files.</li> <li>A further .csv file contains metadata relating to demographic, hormonal and reproductive parameters of the study participants (Gill_NicE_view_participant.csv).</li> <li>A series of 13 R scripts (number 01-12, and a general script containing helper functions) are included to analyze the data and generate the figures found in Gill et al. (A text file containing instructions regarding directory structures is also included) as a .zip archive</li> </ul>
Data from: DNA sequence variation among conspecific accessions of the legume Coursetia caribaea reveals geographically localized clades here ranked as species
Coursetia caribaea is geographically and morphologically the most variable species in the genus Coursetia and in the tribe Robinieae (Leguminosae, Papilionoideae). Because of potentially undetected species, we assessed the phylogenetic relationships among the eight taxonomic varieties of C. caribaea. Sampling included nuclear ribosomal internal transcribed spacer sequences from 489 Robinieae accessions representing all varieties of C. caribaea and 38 of the 40 species of Coursetia, in addition to chloroplast trnD-trnT sequences from 186 accessions. Separate and combined phylogenetic analyses resolved a clade of conspecific accessions of the Bolivian C. caribaea var. astragalina as sister to the central Andean Coursetia grandiflora clade. Also distantly related to Coursetia caribaea var. caribaea accessions were those of the coastal Oaxacan C. caribaea var. pacifica, which formed the sister clade to accessions of the central Andean C. caribaea var. ochroleuca. The estimated mean ages of the stem clades for these three lineages, 11, 7.7, and 7.7 Ma, respectively, contrasted to the estimated mean ages of the corresponding crown clades of 0, 0, and 1.5 Ma. The contrasting stem and crown ages suggest that these taxa, appropriately ranked as species, Coursetia astragalina, Coursetia diversifolia, and Coursetia ochroleuca, each have persisted over evolutionary time frames as distinct geographically localized populations in seasonally dry tropical forests and woodlands.
DNA sequence influences hexasome orientation to regulate DNA accessibility
<p>Each .mat file contains selected traces from one or more videos from a single flow cell. The file name contains the concentration of Gal4 used in the experiment. There are 7 variables in the .mat files</p> <p>data - cell array where each element is an Nx2 matrix containing donor, acceptor pixel intensities for each frame.</p> <p>FRET - cell array where each element is a Nx1 matrix containing FRET values for each frame</p> <p>path - cell array where each element is a Nx1 matrix containing the idealized FRET value calculated from vbFRET</p> <p>path2D - cell array where each element is an Nx2 matrix containing idealized intensities for donor and acceptor from vbFRET (not used)</p> <p>thigh - high fret state dwell times</p> <p>tlow - low fret state dwell times. </p> <p>We also include a matlab progam, TracesView2, that can be used to scroll through the traces.</p>
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis. in Description of the lucky Cophyla (Microhylidae, Cophylinae), a new arboreal frog from Marojejy National Park in north-eastern Madagascar
APPENDIX. GenBank accession numbers of all DNA sequences of Cophyla used in this study. NA, not applicable. Asterisks mark cases where sequences from different samples were combined to chimeric terminals for analysis.
FIGURE. Median network analyses (MNA) of a subset of the C. trilobus aggregate (i.e. those in the clade A from Fig. 11) based on concatenated DNA sequence data from ITS, trnL-trnF and psbJ-petA. Stars and arrow indicate accessions discussed in the text. NI: North Island, SI: South Island. in Five new species of Corybas (Diurideae, Orchidaceae) endemic to New Zealand and phylogeny of the Nematoceras clade
FIGURE. Median network analyses (MNA) of a subset of the C. trilobus aggregate (i.e. those in the clade A from Fig. 11) based on concatenated DNA sequence data from ITS, trnL-trnF and psbJ-petA. Stars and arrow indicate accessions discussed in the text. NI: North Island, SI: South Island.
Systematic review of marine environmental DNA metabarcoding studies: Toward best practices for data usability and accessibility
<p>The emerging field of environmental DNA (eDNA) research lacks universal guidelines for ensuring data produced are FAIR–findable, accessible, interoperable, and reusable–despite growing awareness of the importance of such practices. In order to better understand these data usability challenges, we systematically reviewed 60 peer-reviewed articles conducting a specific subset of eDNA research: metabarcoding studies in marine environments. For each article, we characterized approximately 90 features across several categories: general article attributes and topics, methodological choices, types of metadata included, and availability and storage of sequence data. Analyzing these characteristics, we identified several barriers to data accessibility, including a lack of common context and vocabulary across the articles, missing metadata, supplementary information limitations, and a concentration of both sample collection and analysis in the United States. While some of these barriers require significant effort to address, we also found many instances where small choices made by authors and journals could have an outsized influence on the discoverability and reusability of data. Promisingly, articles also showed consistency and creativity in data storage choices as well as a strong trend toward open access publishing. Our analysis underscores the need to think critically about data accessibility and usability as marine eDNA metabarcoding studies, and eDNA projects more broadly, continue to proliferate.</p>
Systematic review of marine environmental DNA metabarcoding studies: Toward best practices for data usability and accessibility
Open the record for dataset details and reuse information.
Data from: DNA sequence variation among conspecific accessions of the legume Coursetia caribaea reveals geographically localized clades here ranked as species
Open the record for dataset details and reuse information.
Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana
GEO Series GSE20340. Arabidopsis thaliana. 18 samples. Type: Genome variation profiling by array.
Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (ATAC-seq)
GEO Series GSE146616. Mus musculus. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Effect of the NuRD subunit CHD4 on DNA accessibility in Ewing sarcoma cells [ATAC-seq]
GEO Series GSE224002. Homo sapiens. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Landscape of Monoallelic DNA Accessibility and Gene Regulatory Networks during Reprogramming to Naive Pluripotency and X Chromosome Reactivation [ATAC-seq]
GEO Series GSE153844. Mus musculus. 6 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Changes in DNA Methylation Hallmark Alterations In Chromatin Accessibility And Gene Expression For Eye Lens Differentiation [Bisulfite-seq]
GEO Series GSE196629. Gallus gallus. 6 samples. Type: Methylation profiling by high throughput sequencing.
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
GEO Series GSE109828. Homo sapiens. 32 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Effects of DNA topoisomerase inhibitor acriflavine on endothelial gene expression and chromatin accessibility (ATAC-Seq)
GEO Series GSE176554. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Unified analysis of DNA methylation, hydroxymethylation and chromatin accessibility through targeted DNA labeling [TOP-Seq]
GEO Series GSE231928. Mus musculus. 9 samples. Type: Other.
Genome-wide DNA accessibility maps and differential gene expression using ChIP-seq, ATAC-seq and RNA-seq for the human secondary fibroblast cell line hiF-T and whole worms with and without knockdown o
GEO Series GSE98758. Caenorhabditis elegans; Homo sapiens. 58 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
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OpenNeuro
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