Find research datasets worth reusing

opencc-by-4.0Oct 2024View details →

Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplification and flow cytometry

This dataset contains the raw data that were used for the publication entitled, "Ultrasensitive detection of cancer-associated nucleic acids and mutations by primer exchange reaction-based signal amplificaiton and flow cytometry" published in Biosensors and Bioelectronics on 5 October 2024.

opencc-by-4.0Oct 2024View details →

Gut Analysis Toolbox: Data and code associated with JCS manuscript

The data and python code in jupyter notebooks are associated with the manuscript: Sorensen et al. Gut Analysis Toolbox: Automating quantitative analysis of enteric neurons. J Cell Sci 2024; jcs.261950. doi: <a href="https://doi.org/10.1242/jcs.261950" target="_blank" rel="noopener">https://doi.org/10.1242/jcs.261950</a> <ul> <li>FigS1_analysis.zip: Data files (csv) and jupyter notebooks (ipynb) pertaining to Fig. S1D,E.</li> <li>Fig3_analysis.zip: Data files (csv) and jupyter notebooks (ipynb) pertaining to Fig. 3D-N. <ul> <li>The images and analysis files associated with analysis in GAT are also uploaded: CalR_CalB_GAT_analysis.zip</li> <li>The images used in this analysis are from EXP174 in this dataset: <a href="https://zenodo.org/records/7236748">https://zenodo.org/records/7236748</a></li> </ul> </li> </ul>

opencc-by-4.0Jun 2024View details →

Supplementary Materials associated with paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships'

This is a repository for coverage depth graphs and ML-phylogenetic trees that are associated with the paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships' by Tan KC, Collins AG and Ames CL.

opencc-by-4.0Oct 2024View details →

Characterization of Metabolism Associated with Outcomes in Severe Acute Pancreatitis: Insights from Serum Metabolomic Analysis

1H NMR spectra data of SAP patients (Survivors/ Non-survivors). The spectra were binned as 0.02 ppm spectral buckets. The chemical shift regions corresponding to the water region and TSP were excluded to avoid spectral interference. This dataset was used for the metabolomics related study to highlight the dysregulation of metabolites in the study group.

opencc-by-4.0Jun 2021View details →

PhasAGE Expert Seminar- Inhibition of age-associated genomic instability: emerging strategy to delay cellular senescence and aging

The PhasAGE Expert Seminars consist of a series of talks with speakers from PhasAGE partner’s institutions to promote a successful transfer of knowledge about PhasAGE topics – biomolecular phase separation, aging and age-related diseases.

opencc-by-4.0May 2021View details →

GWAS to single cell: Intersecting single-cell transcriptomics and genome wide association studies identifies crucial cell-populations and candidate genes for atherosclerosis.

Background Genome-wide association studies (GWAS) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to identification of candidate genes. However, the assayed tissues are often non-diseased and heterogeneous in cell composition confounding the candidate prioritization. We collected single-cell transcriptomics (scRNA-seq) from atherosclerotic plaques and aimed to identify cell-type-specific expression of disease-associated genes.    Methods and Results To identify disease-associated candidate genes, we applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic, cardiometabolic, and other traits. Next we intersected these candidates with single-cell transcriptomics (scRNA-seq) to identify those genes that are specifically expressed in individual cell (sub)populations of atherosclerotic plaques. We derive an enrichment score and show that loci that associated with coronary artery disease demonstrated a prominent substrate in plaque smooth muscle cells (SKI, KANK2, SORT1), endothelial cells (SLC44A1, ATP2B1), and macrophages (APOE, HNRNPUL1). Further sub clustering of SMC-subtypes revealed genes in risk loci for coronary calcification specifically enriched in a synthetic cluster of SMCs. To verify the robustness of our approach, we used liver-derived scRNAseq-data and showed enrichment of circulating lipids-associated loci in hepatocytes. Conclusion We confirm known gene-cell pairs relevant for atherosclerotic disease, and discovered novel pairs pointing to new biological mechanisms amenable for therapy. We present an intuitive single-cell transcriptomics driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits.

Processed data used in transcriptome- metabolome-wide association study

Processed_RNASeq_RPKM.txt contains RPKM levels for 45484 genes quantified in 555 individuals from RNA-Seq of lymphoblastoid cell lines (LCLs). Processed_NMRpeaks_baseline.txt contains binned, normalized and standardised (z-scored) NMR peak intensities for 1276 bins quantified in 555 individuals from urine samples taken at baseline. NMR spectra were acquired at 300 K on a Bruker 16.4 T Avance II 700 MHz NMR spectrometer (Bruker Biospin, Rheinstetten, Germany) using a standard 1H detection pulse sequence with water suppression. The spectra were referenced to the TSP signal and phase and baseline corrected. Processed_NMRpeaks_followup.txt contains binned, normalized and standardised (z-scored) NMR peak intensities for 1289 bins quantified in 315 individuals from urine samples taken during follow-up. NMR spectra were acquired with an Avance III HD 600 NMR spectrometer. Spectra were referenced to the TSP signal and phase and baseline corrected. More details on the data set can be found in Sönmez Flitman et al. (doi: https://doi.org/10.1101/2020.05.22.110197).

opencc-by-3.0-usJul 2021View details →

GDC-PANCAN.htseq_counts and associated meta-data no longer available from gdc.xenahubs.net

The RNA-seq data and associated meta-data I used for my publications, downloaded from gdc.xenahubs.net but no longer available in this form (i.e. raw counts) from the website.

Building Large-Scale Gene-Disease Association Datasets for Biomedical Relation Extraction

This repository contains the GDAb and GDAt datasets. GDAb and GDAt are large-scale, distantly supervised, and manually enhanced datasets for Gene-Disease Association (GDA) extraction. Each dataset consists of three text files, corresponding to train, validation, and test sets, plus an additional JSON file containing the mapping between relation names and IDs. Each record in train, validation, or test files corresponds to a single GDA extracted from a sentence. Records are represented as JSON objects with the following structure: <ul> <li>text: sentence from which the GDA was extracted.</li> <li>relation: relation name associated to the given GDA.</li> <li>h: JSON object representing the gene entity, composed of: <ul> <li>id: UMLS CUI associated to the gene entity.</li> <li>name: UMLS preferred name associated to the gene entity.</li> <li>pos: list consisting of starting position and length of the gene mention within text.</li> </ul> </li> <li>t: JSON object representing the disease entity, composed of: <ul> <li>id: UMLS CUI associated to the disease entity.</li> <li>name: UMLS preferred name associated to the disease entity.</li> <li>pos: list consisting of starting position and length of the disease mention within text.</li> </ul> </li> </ul> Both datasets contain over 2,500,000 sentences and 500,000 bags. The zip file consists of two folders, GDAb and GDAt,  containing the files corresponding to the two datasets, respectively.

UAV outputs and associated field measurement of the herbaceous and tree of the Senegalese savanna of the Dahra Djoloff research center

The dataset contains UAV outputs (mosaic , surface model and terrain) and the associated measurements of vegetation( herbaceous and woody) that were made within the research isra station of Dahra Djoloff. Sites The sites were 38 ha-1 plots across the research station. The UAV were collected on the same site at the same date in October 2018(end of the wet season and maximum of the biomass). The sites were the sites of previous studies (Raynal 1964, Ndiaye et al. 2014, Ndiaye et al. 2015). The plots were chosen based on several studies of vegetation dynamics and these plots were judged to be representative of the diversity of vegetation type within the research station. UAV flight plan We used a low-cost UAV with an RGB (Red Green Blue) captor integrated in the UAV. The plots were mapped using a Dji Spark UAV with the litchi application for the automatic flight. The flight plan was six 100 m transects each separated by 20 m was performed at an altitude of 80 m and at a speed of 5 m.s-1. Images were acquired in autofocus mode (ISO exposure were automatically adjusted) at two-second intervals throughout the flight. The angle of view was 80°. The frontal overlap was about 90% and the side overlap about 80% with 80° angle Field measurement. Herbaceous Biomass. For the Landscape dataset, 10 squares of 1 m² were sampled; All the aboveground biomass was cut and weighted in fresh. A composite sample was made for each site and weighted dry to evaluated the dry matter content and so the dry matter of each sample. The positions of the squared was mark r with a plastic bag on the ground. Tree measurement. For the landscape, we selected 10 trees on the UAV maps. The measurements were made after image analysis in January 2019 and January 2020. The trees were not measured on all the site. The measured variables were the maximum height of the tree (using a clinometer), the diameter of the tree crown in the north-south direction and in the west-east direction. Their tree crown area was calculated assuming that the crown was a circle. The trunk diameters were measured at 0.30 cm in both direction and the circumference were calculated. All woody species were identified at the species and genus levels. Image analysis. The images taken during each flight were processed using a PiX4D mapper (Pix4D SA, Lausanne, Switzerland). 3D mapping is the basic parameter proposed in the software. For each plot, an orthophotograph, a digital surface model, and a digital elevation model were computed and exported in GeoTIFF format. Data organization For each plot, we had <ul> <li>DSM that contains the surface model in tiff</li> <li>DTM that contains the terrain model in tiff</li> <li>Mosaic that the orthomosaic in tiff.</li> </ul> All the different geotiff can directly be download. Data are in a zip file that contains the shapefile with the position and table with the field measurements. The shapefile “Herbaceous.shp” contain the positions of the squared sample but also of squared that contains only soil (squared cut before the flight). The CSV “Herbaceous-landscape.csv” contains the measurement of Aboveground biomass. (FM fresh mass and DM dry mass). Both are in g (g.m-²). The biomass was available for 346 squared. The shapefile “tree.shp” contains the positions of the tree. Here the shapefile contains the positions of all the tree preselected on the map. Only a selection of theses tree was measured on the field. The file “Tree-landscape.csv” contains the tree measurements with the species, the height (in m), the trunk circumference (TC) in cm and the area of the crown(area) in m². The tree measurements were available for 240 trees.   reference Ndiaye, O., A. T. Diop, L. E. Akpo, and M. Diène. 2014. Dynamique de la teneur en carbone et en azote des sols dans les systèmes d’exploitation du Ferlo: cas du CRZ de Dahra. Journal of Applied Biosciences 83:7554-7569. Ndiaye, O., A. T. Diop, M. Diène, and L. E. Akpo. 2015. Étude comparée de la végétation de 1964 et 2011 en milieu pâturé: Cas du CRZ de Dahra. Journal of Applied Biosciences 88:8235–8248. Raynal, J. 1964. Etude botanique de pâturages du Centre de Recherches Zootechniques de Dahra-Djoloff (Sénégal).

UAV outputs and associated field measurement of the herbaceous and tree of the Senegalese savanna across Senegal

This dataset contains UAV outputs (mosaic, surface and terrain model) and field measurement of vegetation that were made in northern and Eastern Senegal. Sites National gradient measurements For the national gradients, the measurements were made on 45 different plots in two different field campaign. One in the Northern part at the end of September 2020 and the other in South eastern part of Senegal in middle of October. The selection of the site was a combination of accessibility (not far from the road) and diversity of vegetation. The average rainfall for the period 1981-2018 was ranging from 221 mm.y-1 to 468 mm. y-1 for the Northern Part and ranging 759 mm.y-1 to 1246 mm y-1 for the south eastern part. UAV flight plan We used a low-cost UAV with an RGB (Red Green Blue) captor integrated in the UAV.  The UAV was an Anafi of Parrot with PIX4D capture application using the double gird flight plan in a square generally of 100m*100m; The height of the flight was 80m with an overlap of 80% at low speed with 80° angle °.  The flights were made at any time during the day. Field measurement. Herbaceous Biomass. 3 squares of 1 m² were sampled. All the aboveground biomass was cut and weighted in fresh. A composite sample was made for each site and weighted dry to evaluated the dry matter content and so the dry matter of each sample. The height of 5 herbaceous individuals selected randomly were measured. We recorded the species composition with percentage of cover of each species. We collected an herbarium sample each time we had a new species. The sample were used to identified the species by the IFAN herbarium team. The positions of the squared was mark with a wood triangle painted on the ground. Tree measurement. Four trees were measured on the field. It was the four woody individuals the closest to the first square of herbaceous measurements were made in each direction (Northwest, North east, South West, South East). The distance to the first square of each tree were measured using a telemeter. The height was also measured with a laser telemeter. The circumference at 0.30cm and 1.3 cm were measured. The diameter of the tree crown in the north-south direction and in the west-east direction were measured to the crow area calculated assuming that the crown was a circle. The species were recorded. We collected an herbarium sample each time we had a new species. The sample were used to identified the species by the IFAN herbarium team. Image analysis. The images taken during each flight were processed using a PiX4D mapper (Pix4D SA, Lausanne, Switzerland). 3D mapping is the basic parameter proposed in the software. For each plot, an orthophotograph, a digital surface model, and a digital elevation model were computed and exported in GeoTIFF format. Data organization The data are organized in two separated folders for each dataset. Each dataset folders contains four folders: <ul> <li>DSM that contains the surface model in tiff</li> <li>DTM that contains the terrain model in tiff</li> <li>Mosaic that the orthomosaic in tiff.</li> <li>Data that contains the shapefile with the position and table with the field measurements.</li> </ul> The shapefile” national-shape.shp" contains the positions of both tree and herbaceous samples. In some case it was hard to position the squared or the tree. The position and the shape of the object are not well defined. The file “tree-national.xlsx” contains the information on the tree measurement. The ID that contains the site and the positions of the trees, the distance from the squared in m that indicate the distance of the tree to the biomass square. The height H (in m), the trunk circumference at 1.30m (TC1.3) and at 0.3m(TC0.3) in cmand the area of crown (Area). The species is also described. The file “ herbacous_national.xlsx” contains the information on the herbaceous layer. For each square, the height of the herbaceous layer (H), Fresh mass (FM), Dry matter content (DMC) and dry Mass (DM) are presented; The last columns of the file are the different species with the percentage of cover in each case.

opencc-by-4.0Aug 2021View details →

Data Files and Code Associated with "Brown Dwarfs are Violet"

The accompanying files provide some IDL code and "data behind the figures" for the paper titled "Brown Dwarfs are Violet" (by S. R. Cranmer), which has been submitted to Research Notes of the AAS. This paper presents a collection of objective (CIE x,y coordinate) and subjective (RGB triple) colors for main-sequence stars and brown dwarfs, as they may be perceived by human eyes without the reddening effects of the Earth's atmosphere.  However, the algorithm described in the paper for computing RGB triples ought to be considered as only a preliminary first step; i.e., it needs to be tested by comparing the results to other more established ways of converting astronomical spectra to perceived colors.

opencc-by-4.0Sep 2021View details →

Data and code associated with manuscript by Gibert et al

This is the code and data associated with the article :"Non-reproducible signals of adaptation to elevation between light and shade environments in Snapdragon plants" by Gibert et al published in Journal of Evolutionary Biology

opencc-by-4.0Oct 2022View details →

DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids

This dataset contains the raw data that were used for the publication entitled, "DNA origami book biosensor for multiplex detection of cancer-associated nucleic acids" published in Nanoscale.   Abstract DNA nanotechnology provides a promising approach for the development of biomedical point-of-care diagnostic nanoscale devices that are easy to use and cost-effective, highly sensitive and thus constitute an alternative to expensive, complex diagnostic devices. Moreover, DNA nanotechnology-based devices are particularly advantageous for applications in oncology, owing to being ideally suited for the detection of cancer-associated nucleic acids, including circulating tumor-derived DNA fragments (ctDNAs), circulating microRNAs (miRNAs) and other RNA species. Here, we present a dynamic DNA origami book biosensor that is precisely decorated with arrays of fluorophores acting as donors and acceptors and also fluorescence quenchers that produce a strong optical readout upon exposure to external stimuli for the single or dual detection of target oligonucleotides and miRNAs. This biosensor allowed the detection of target molecules either through the decrease of Förster resonance energy transfer (FRET) or an increase in the fluorescence intensity profile owing to a rotation of the constituent top layer of the structure. Single-DNA origami experiments showed that detection of two targets can be achieved simultaneously within 10 min with a limit of detection in the range of 1–10 pM. Overall, our DNA origami book biosensor design showed sensitive and specific detection of synthetic target oligonucleotides and natural miRNAs extracted from cancer cells. Based on these results, we foresee that our DNA origami biosensor may be developed into a cost-effective point-of-care diagnostic strategy for the specific and sensitive detection of a variety of DNAs and RNAs, such as ctDNAs, miRNAs, mRNAs, and viral DNA/RNAs in human samples.

Migration on the Chessboard: Political Violence as a Decisive Factor in Coercive Migration Diplomacy (Data and Associated Files for Dissertation)

This publication contains files associated with analysis for my dissertation, "Migration on the Chessboard: Political Violence as a Decisive Factor in Coercive Migration Diplomacy." The dissertation explores a potential relationship between political violence and a state leader's choice to use migration as a bargaining chip in pursuit of foreign policy objectives. "Key to datasets.docx" and "dataframes_viz.png" explain the contents of the five datasets used. These five datasets are the five .dta files. There are five log files (.txt) and five do files containing code (.do) corresponding to the five datasets. Finally, each dataset has three associated results tables (.xls) for a total of fifteen .xls files.

Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis

Mycobacterium avium is one of the prominent disease-causing bacteria in humans. It causes lymphadenitis, chronic and extrapulmonary, and disseminated infections in adults, children, and immunocompromised patients. M. avium has ~4,500 predicted protein-coding regions on an average, which can be helpful in discovering several variants at the proteome level. Many of them are potentially associated with virulence, thus identifying such proteins can be a helpful feature in the development of panel-based theranostics. In line with such a long-term goal, we carried out an in-depth proteomic analysis of M. avium with both data-dependent and data-independent acquisition methods. Further, a set of proteogenomic investigations were carried out using the protein database for Mycobacterium tuberculosis, and a genome six-frame translated database and a variant protein database of M. avium. A search of mass spectrometry data analysis against M. avium protein database resulted in the identification of 2,954 proteins. Further, proteogenomic analyses aided in the identification of 1,301 novel peptide sequences and correction of translation start sites for 15 proteins. At the end, we created a spectral library of M. avium proteins including novel genome search-specific peptides and variant peptides detected in this study. We validated the spectral library by a data-independent acquisition of the M. avium proteome. Thus, we present a M. avium spectral library of 29,033 peptide precursors supported by 0.4 million fragment ions for further use by the biomedical community.

Mycobacteroides abscessus subp. bolletii strain associated with a persistent infection (genome assembly and annotation dataset)

This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) of a Mycobacteroides abscessus subp. bolletti strain associated with a persistente infection. (genome anotation was performed using Bakta v1.2.2 https://github.com/oschwengers/bakta) The raw sequence reads were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB57933; Run Accession: ERR10554471).

Data for Li et al., Waterborne virus transport and the associated risks in a large lake, Water Research; DOI: 10.1016/j.watres.2022.119437

Experimental data (virus concentrations measured in sewage, in units of genome copies per mL sewage)  Code (written in R) used to model virus concentration distributions Code (Delft3D and Matlab) used for hydrodynamic, water quality and QMRA simulations. Input files are for the "winter scenario" shown in the publication.

opencc-by-4.0Aug 2022View details →

Data associated with "Developing a standardized but extendable framework to increase the findability of infectious disease datasets"

Data associated with "Developing a standardized but extendable framework to increase the findability of infectious disease datasets"   Includes: <ul> <li>NIAID Dataset schema</li> <li>NIAID ComputationalTool schema</li> <li>Crosswalk between NIAID schemas and common schemas</li> <li>Survey of Schema.org-compliant repositories</li> </ul> The open access movement and scientific reproducibility concerns have led the biomedical research community to embrace efforts to make scientific datasets openly accessible. While many datasets are now available, there are still challenges in ensuring that they are Findable, Accessible, Interoperable, and Reusable (FAIR). To improve the FAIRness of datasets, we evaluated dataset repositories for compliance with Schema.org standards – a collection of standards developed to increase metadata searchability across the internet. Adoption of the Schema.org Dataset standard was highly variable in biomedical research datasets, and the standard omitted many desirable metadata fields. We customized the Schema.org Dataset standard to catalog datasets collected across a Systems Biology research consortium consisting of 15 Centers. We developed a reusable process for creating a schema which is interoperable with other standards, but still extendable and customizable to a particular context. Here, we describe our process along with the associated gains in FAIRness, and discuss ongoing challenges with dataset discoverability – the first step to ensure that the vast amount of open data published by the research community is reused to its maximum value.