Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
33
datasets available to search
ShareScore release 0.9.0
Dataset results
33 results for “DNA topology”
Topological Overlap Matrices for DNA Methylation data of Gestational Diabetes Cohort with BMI and Exposure Status
<p>DNA methylation in placenta was measured with the Infinium HumanMethylation450 BeadChip (Illumina, Inc) microarray, in a sample of 28 women, 20 of whom had a gestational diabetes (GD)-affected pregnancy and 8 who did not. We used GD status as our exposure variable, assuming that this has widespread effects on DNA methylation and on its correlation patterns. Our response, Y, is the standardized body mass index (BMI) in the offspring at the age of 5. For the 10,000 most variable probes, we provide 3 topological overlap matrices (TOM), which are used in our analysis (note that each of the following TOM matrices are a 10,000 by 10,000 symmetric matrix with row names and column names corresponding to the CpG probe IDs:</p> <ol> <li>TOM_Methylation_All_10k.rds: based on all 28 subjects, </li> <li>TOM_Methylation_E0_10k.rds: based on the 8 subjects without a GD-affected pregnancy</li> <li>TOM_Methylation_E1_10k.rds: based on the 20 subjects with a GD-affected pregnancy </li> </ol> <p>The BMI (phenotype) and GD status (exposure) are given in the following dataset:</p> <ol> <li>BMI_and_Exposure_Status.rds: 28 x 2 matrix of the phenotype and exposure. each row is a subject.</li> </ol> <p>Using our ECLUST method (preprint available at http://sahirbhatnagar.com/slides/manuscript1_SB_v4.pdf), we derive 77 clusters, and here we provide the 1st principal component of each cluster:</p> <ol> <li>Cluster_Summary_1stPC.rds: 28 x 77 matrix, where each row is a subject, in the same order as the BMI_and_Exposure_Status.rds data</li> <li>Cluster_CpGs_names.rds: a list of length 77, where each element of the list contains the list of CpG probe IDs contained in each of the clusters</li> </ol> <p>To read in the data use the readRDS function, e.g.:</p> <p>TOM_All <- readRDS(file = "TOM_Methylation_All_10k.rds")</p>
The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
<p>Metabarcoding of environmental DNA constitutes a state-of-the-art tool for environmental studies. One fundamental principle implicit in most metabarcoding studies is that individual sample amplicons can still be identified after being pooled with others – based on their unique combinations of tags – during the so-called demultiplexing step that follows sequencing. Nevertheless, it has been recognized that tags can sometimes be changed (i.e. tag jumping), which ultimately leads to sample crosstalk. Here, using four DNA metabarcoding datasets derived from the analysis of soils and sediments, we show that tag jumping follows very specific and systematic patterns. Specifically, we find a strong correlation between the number of reads in blank samples and their topological position in the tag matrix (described by vertical and horizontal vectors). This observed spatial pattern of artefactual sequences could be explained by polymerase activity, which leads to the exchange of the 3' tag of single stranded tagged sequences through the formation of heteroduplexes with mixed barcodes. Importantly, tag jumping substantially distorted our datasets – despite our use of methods suggested to minimize this error. We developed a topologic model to estimate the noise based on the counts in our blanks, which suggested that 40-80% of the taxa in our soil and sedimentary samples were likely false positives introduced through tag jumping. We highlight that the amount of false positive detections caused by tag jumping strongly biased our community analyses. </p>
The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
Open the record for dataset details and reuse information.
Data from: Topological DNA-binding of SMC-like RecN promotes RecA-mediated DNA double-strand break repair
<p>Bacterial RecN, closely related to the structural maintenance of chromosomes (SMC) family of proteins, functions in the repair of DNA double-strand breaks (DSBs) by homologous recombination. However, the understanding of how RecN acts in concert with the RecA recombinase to promote DSB repair remains limited. Here, we demonstrated that the purified Escherichia coli RecN protein topologically loads onto both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) that has a preference for ssDNA. RecN topologically bound to dsDNA slides off the end of linear dsDNA, but this is prevented by RecA nucleoprotein filaments on ssDNA, thereby allowing RecN to translocate to DSBs. Furthermore, we found that, once RecN is recruited onto ssDNA, it can topologically capture a second dsDNA substrate in an ATP-dependent manner, suggesting a role in synapsis. Indeed, RecN stimulates RecA-mediated D-loop formation and subsequent strand exchange activities. Our findings provide mechanistic insights into the recruitment of RecN to DSBs and sister chromatid interactions by RecN, both of which function in RecA-mediated DSB repair.</p>
Two type I topoisomerases maintain DNA topology in human mitochondria
<p>Raw image data from the article "Two type I topoisomerases maintain DNA topology in human mitochondria" by Katja E. Menger et al.</p>
Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations: Simulations Topology, Coordinate, Parameters, Input and Output files
<p>The simulation data for the article: Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.</p> <p>ck_metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations with different c(K+), which are newly added runs for resubmission. The corresponding script files and Plumed files are in GitHub.</p> <p>eq_mini.tar.gz: Includes the parameter files required for the equilibration and minimization protocol.</p> <p>standard_md.tar.gz: Includes the topology files and coordinate files for all systems built in the article. Also include the hbfix parameters file required on the MD run, and the MD script file.</p> <p>metad.tar.gz: Includes the topology files, coordinates files and gromacs parameter input file (.mdp) used for WT-MetaD-HREX simulations. The corresponding script files and Plumed files are in GitHub.</p> <p>metad*fe*.tar.gz: Plumed HILLS files and metad.bias data used for drawing the free energy landscapes.</p> <p>ions.tar.gz: Data used for Figure.3 in the manuscript</p> <p>si_data.tar.gz: All data used for SI figures.</p>
Data from: Topological DNA-binding of SMC-like RecN promotes RecA-mediated DNA double-strand break repair
Open the record for dataset details and reuse information.
Data from: Topological, chemical, and electro-optical characteristics of riboflavin-doped artificial and natural DNA thin films
DNA is considered as a useful building bio-material, and it serves as an efficient template to align functionalized nanomaterials. Riboflavin (RF)-doped synthetic double-crossover DNA (DX-DNA) lattices and natural salmon DNA (SDNA) thin films are constructed using substrate assisted growth and drop-casting methods, respectively, and their topological, chemical, and electro-optical characteristics were evaluated. The critical doping concentration of RF ([RF]C, ~5 mM) at given concentrations of DX-DNA and SDNA were obtained by observing the phase transition (from crystalline to amorphous structures) of DX-DNA and precipitation of SDNA in solution above [RF]C. [RF]C are verified by analyzing the atomic force microscopy images for DX-DNA and current, absorbance, and photoluminescence for SDNA. We study the physical characteristics of RF-embedded SDNA thin films, which are the Fourier transform infrared (FTIR) spectrum to understand the interaction between the RF and DNA molecules, current to evaluate the conductance, absorption to understand the RF binding to the DNA, and photoluminescence (PL) to analyze the energy transfer between the RF and DNA. The current and UV absorbance band of SDNA thin films decrease up to [RF]C followed by an increase above [RF]C. In contrast, the PL intensity illustrates the reverse trend, as compared to the current and UV absorbance behavior as a function of the varying [RF]. Due to the intense PL characteristic of RF, the DNA lattices and thin films with RF might offer immense potential to develop efficient bio-sensors and useful bio-photonic devices.
Data from: Topological, chemical, and electro-optical characteristics of riboflavin-doped artificial and natural DNA thin films
Open the record for dataset details and reuse information.
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.
DNA topology analysis reveals stable compartments and TADs in malignant and normal uveal melanocytes as novel molecular features of uveal melanoma
GEO Series GSE201727. Homo sapiens. 5 samples. Type: Other.
Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression
GEO Series GSE123373. Mus musculus. 116 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene [array]
GEO Series GSE77587. Streptococcus pneumoniae R6. 8 samples. Type: Expression profiling by array.
Analysis of the DNA topology in T47D-MTVL cells by Hi-C data
GEO Series GSE147627. Homo sapiens. 1 samples. Type: Other.
Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (RNA-seq)
GEO Series GSE146668. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (ChIP-Seq)
GEO Series GSE123371. Mus musculus. 62 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (Bisulfite-Seq)
GEO Series GSE138613. Mus musculus. 12 samples. Type: Methylation profiling by high throughput sequencing.
DNA topological regulation by topoisomerase IIβ-DNA-PK interaction is important for controlled hypoxia-inducible gene expression [RNA-Seq]
GEO Series GSE285698. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Mutational synergy coordinately remodels chromatin accessibility, enhancer landscape and 3-Dimensional DNA topology to alter gene expression during leukemia induction (pCHiC)
GEO Series GSE146662. Mus musculus. 10 samples. Type: Other.
Analysis of the DNA topology upon multiple histone H1 variants depletion by Hi-C experiments
GEO Series GSE172618. Homo sapiens. 6 samples. Type: Other.
ScienceDex guides
Understand access before you commit
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)
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.