Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

Multiplexed single-cell characterization of alternative polyadenylation regulators (HEK293FT & K562 Perturb-seq data)

This site provides access to datasets from the CPA-Perturb-seq <a href="https://www.biorxiv.org/content/10.1101/2023.02.09.527751v1">manuscript</a> Kowalski*, Wessels*, Linder* et al., including processed Perturb-seq datasets from HEK293FT and K562. We release these data as Seurat objects, where each object contains single-cell quantifications of gene expression (RNA assay), and in addition, quantifications of polyA site usage (polyA site assay). To explore these data, please install the <a href="https://github.com/satijalab/PASTA">PASTA</a> (PolyA Site analysis using relative Transcript Abundance) package, which provides infrastructure and analytical tools to explore alternative polyadenylation at single-cell resolution. For each dataset, we also include a fragment file which enables visualization of read coverage plots across groups of cells.  The files include: 1. CPA_K562.Rds : Seurat object containing the K562 CPA-Perturb-seq dataset  2. CPA_K562_fragments.tsv.gz : Fragment file for the K562 dataset  3. CPA_K562_fragments.tsv.gz.tbi : Fragment file index for the K562 dataset    R code below: <pre><code>library(PASTA) k562 <- readRDS("CPA_K562.Rds") # Add fragments for plotting  Fragments(k562) <- CreateFragmentObject(path = "download/CPA_K562_blocks.tsv.gz", cells = Cells(k562)) # visualize polyA site usage PolyACoveragePlot(k562, region ="chr7-26212195-26213351")</code></pre>

opencc-by-4.0Sep 2024View details →

Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes

Supplementary dataset to the manuscript: Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes, by Mauricio Andino-Molina, Mostafa Abdel-Glil, Fanny Hidalgo-Villeda, Edgardo Tzoc, Gernot Schmoock, Mathias W. Pletz, Heinrich Neubauer & Christian Seyboldt.  Dataset analysed with clostyper (https://gitlab.com/FLI_Bioinfo/clostyper)

opencc-zeroOct 2023View details →

Characterization of leaf transcriptome in a tropical tree species, Shorea curtisii, over a flowering season

General flowering (GF) is a synchronous flowering event in the Southeast Asian tropical rainforests that occurs at irregular intervals of multiple years. The unpredictable intervals of GF raise conservation concerns for these under-researched forests with rich economically and ecologically important species. In this study, the leaf transcriptome of a GF species, Shorea curtisii obtained from three time points – before and after floral initiation, and post flowering stage – was sequenced. We assembled 243,759,478 sequencing reads into 39,943 non-redundant unigenes including 677 putative homologs of Arabidopsis thaliana flowering-related genes. Differential expression analysis conducted on pairwise comparisons of the time points identified 930 differentially expressed unigenes, which includes 17 flowering-related homologs. The differential expression of unigenes with significant enrichments of functions related to drought corroborated the involvement of drought as an environmental cue for GF. The outcomes of this study offer an insight into the conservation of floral regulatory genes and pathways in Shorea and could be used as a model to better understand the floral initiation cues and regulation of GF trees.

opencc-by-4.0Oct 2023View details →

Scan tiles obtained through Confocal Laser Scanning Microscopy for roughness characterization of surfaces

The Data includes all the original data collected from individual scan tiles of both quartz and glass surfaces using Confocal Laser Scanning Microscopy.  The techniques used for merging scan tiles linearly, as well as the procedures for data processing and analysis, are detailed in the methods and results sections of this manuscript. A sperate methods section include along with data files also describe the details of the Image acquisition, preprocessing, and tiling methodology.

Compositional Characterization of Glassy Volcanic Material From VNIR and MIR Spectra Using Partial Least Squares Regression Models

This is supporting data for the paper titled "Compositional Characterization of Glassy Volcanic Material From VNIR and MIR Spectra Using Partial Least Squares Regression Models" by Leight et al. (submitted to JGR-P 11/23). Table S1 lists each spectrum used to train PLS models, its source, and which training datasets the spectrum was included in. Zip files contain the MIR and VNIR PLS model files. Model files are .asc, and can be run using the code at Ytsma, (2022), https://doi.org/10.5281/zenodo.7347345.

Characterizing ambient air quality and oil and gas air pollution emissions in Broomfield County, CO

Unconventional oil and natural gas development (UOGD) has expanded rapidly across the United States in recent decades and raised concerns about associated air quality impacts. While significant effort has been made to quantify methane emissions, relatively few observations have been made of Volatile Organic Compounds (VOCs), especially during drilling and completion of new wells. Extensive air monitoring during development of several large, multi-well pads in Broomfield, Colorado, in the Denver-Julesburg Basin, provides a novel opportunity to examine changes in local air toxics and other VOC concentrations during well drilling and completions and production.

opencc-by-4.0Feb 2022View details →

[DATASET 1] - BIOMECHANICAL CHARACTERIZATION OF SELECTED CLIMBING PLANTS

In the framework of GrowBot project, Task 3.1 aims at selecting and investigating different climbing plants as models for GrowBot artefacts. The activities consist of biomechanical investigation and the analysis of plants’ functional strategies with respect to environmental complexity in terms of size, shape, density of supports, clutter and presence of voids. Task 3.3 aims at selecting and investigating different climbing plants’ attachment strategies for inspiring the design and development of artificial solutions. DS1 aims at collecting all the experimental data gathered during these activities.

Data from: A pioneering experimental investigation of a novel in-situ dynamic characterization of the tensile/compression stress-strain mechanism on human plantar soft tissue

We have conducted the first in-situ and in-vivo dynamic mechanical test on human plantar soft tissue. A dynamic mechanical analysis (DMA)-like device has been invented to perform the in-situ and in-vivo stress-strain tests on living plantar in order to characterize the material mechanism of biological soft tissue, whereas it is nearly impossible to prepare a sample from a living body for classical tests. A series of pioneering tests of tensile/compression on the heel of ten volunteers are reported, with the reference of tests on mimic foot model made by silicon rubber, standard silicon rubber brick sample, and finite elementary analysis. In addition to demonstrating the effectiveness of the device and approach, interesting correlations between the results and clinic data were found, suggesting considerable potential for the invention in future research.

opencc-by-4.0Oct 2023View details →

Datasets of VAMAS TWA2 Project 33: Chemical characterization of graphene related two-dimensional materials by XPS

The datasets contain excel-files of the XPS raw data of the participants of the interlaboratory comparison. Additionally, the protocol is added.

X-ray beam characterization of an aberration-corrected pair of multilayer Laue lenses with ptychography

This data set is split over three zip archives. Each archive contains a scanning coherent X-ray diffraction (ptychography) data set recorded at an X-ray energy of 16.2 keV. A crossed pair of multilayer Laue lenses (MLL) is used to focus the beam and scan a Siemens star test sample. Each data set includes a configuration file and scan position file. In addition, the final result of the obtained ptychographic reconstruction is included.Description of the three data sets:<ul><li>scan_00086: X-ray beam characterization of the MLL. On this data set the design of the refractive phase corrector was based upon.</li><li>scan_00338: X-ray beam characterization of the MLL four days after scan_00086 without phase corrector.</li><li>scan_00346: X-ray beam characterization of the MLL with refractive phase corrector.</li></ul>Additional information:The diffraction patterns can be found in the 'eiger4m_01' folder. They are split up over multiple h5 files and located in the group '/entry/data/data'. The assignment of diffraction patterns to scan positions can be found in the positions.txt file. All relevant input parameters for ptychography are located in the 'input' group in the ptycho.conf files. The reconstruction results are in the European Data Format (EDF).The data set has been published in:F. Seiboth, A. Kubec, A. Schropp, S. Niese, P. Gawlitza, J. Garrevoet, V. Galbierz, S. Achilles, S. Patjens, M. E. Stuckelberger, C. David, and C. G. Schroer, "Rapid aberration correction for diffractive X-ray optics by additive manufacturing," Optics Express 30(18), 31519 (2022).

Characterizing a lethal mitonuclear incompatibility in naturally hybridizing Xiphophorus swordtails

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of "hybrid incompatibilities," where alleles derived from two different species no longer interact properly in hybrids. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes and that incompatibilities involving multiple genes should be common, but there has been sparse empirical data to evaluate these predictions. Here, we describe a mitonuclear incompatibility involving three genes in physical contact within respiratory Complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations fail to complete embryonic development or die as juveniles, while those heterozygous for the incompatibility have reduced Complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the impacts of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and the first case of an incompatibility transferred between species via hybridization.

Data for "Characterizing quantum gases in time-controlled disorder realizations using cross-correlations of density distributions"

Here, data sets belonging to the preprint "Characterizing quantum gases in time-controlled disorder realizations using cross-correlations of density distributions" are uploaded. The file contains a folder for each figure in the manuscript.

Data for: Fabrication and characterization of antibacterial coatings using an amphoteric condensed tannin,Tanfloc

This dataset presents comprehensive information on the development and characterization of antibacterial polyelectrolyte multilayer (PEM) coatings incorporating tanfloc, a plant-derived condensed tannin polymer with inherent antimicrobial properties. The dataset encompasses experimental data related to the fabrication of PEMs using tanfloc as either a polyanion or a polycation, expanding the versatility of this amphoteric polymer in PEM coatings. Typically, PEMs are formed by combining a polycation and a polyanion with complementary ionic groups. However, the unique amphoteric nature of tanfloc allows for the creation of PEMs utilizing only one of its functional groups, leaving the other functional group available for imparting antibacterial activity. The dataset includes details on the assembly of tanfloc-containing PEMs employing various counter-polyelectrolytes, including three poly-anionic glycosaminoglycans with varying charge densities, as well as the polycations N,N,N-trimethyl chitosan and polyethylenimine. The layer-by-layer assembly of PEMs is monitored using in situ Fourier-transform surface plasmon resonance (FT-SPR), confirming stable layer-by-layer construction. Surface chemistry is assessed through X-ray photoelectron spectroscopy (XPS). Furthermore, this dataset provides insights into the biocompatibility of tanfloc-containing PEMs, demonstrating their support for mammalian cells. Most notably, the dataset includes extensive data on the antiadhesive and antibacterial properties of these coatings against common implant-associated pathogens, such as Staphylococcus aureus and Pseudomonas aeruginosa. The antibacterial effects observed are attributed to electrostatic interactions and the polyphenolic nature of tanfloc.

opencc-by-4.0Oct 2023View details →

ChromoPhyloGen: characterizing copy number alteration patterns in heterogeneous tumor cell populations at Single-Cell Resolution

The human liver cancer cell line Huh7 was obtained from the American Type Culture Collection (ATCC). Huh7 cells were cultivated in Dulbecco's Modified Eagle Medium (DMEM, Gibco, C11995), supplemented with 1% penicillin/streptomycin (Gibco, 15140122), and 10% fetal bovine serum (FBS, Excell, FSP500). Huh7 cell line was maintained under a 95% O2 and 5% CO2 humidified atmosphere in an incubator at 37˚C.  The scDNA-seq library was performed using the Chromium Single cell DNA Library & Gel Bead kit (10x Genomics, PN1000040) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip C and D (10x Genomics, 1000022 and 1000042, respectively) according to the manufacturer's user guide and subsequently run on a thermocycler. The barcoded libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells. The scRNA-seq library was generated using the 10x Genomics Chromium Single Cell 3' & Gel Bead Kit v3 (10x Genomics, PN100075) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip B (10x Genomics,1000154) according to the manufacturer's protocol and subsequently run on a thermocycler. The 3' gene expression libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells.

Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer

All data supporting the publication: "Multiplexed imaging mass cytometry analysis characterizes the vascular niche in pancreatic cancer."1. Fully_Processed_OME.TIFF: This folder contains the OME.TIFF files with all markers after compensation and hot pixel removal for visualization of the data. These can be opened with QuPath and other software. 2. PDAC_IMC_Seurat_FINAL.rds: Seurat object of all cells included in the analysis with cell type and neighborhood annotations, and unintegrated and rPCA-integrated UMAP reductions. 3. Raw_Data_TIFF_Files: All raw individual TIFF files from the image acquisition4. ROI_Selection: Brightfield and IHC images of individual samples showing where the ROIs for each sample are collected 5. Segmentation_Files: All relevant segmentation files from Mesmer for nuclear and whole cell segmentation. 6. H&E Images for each case scanned at 40x

opencc-by-nc-4.0Nov 2023View details →

Figure 2 in Morphological and molecular characterization of Geraldius galapagoensis (Nematoda: Chambersiellidae) associated with lichens in Argentina

Figure 2. ML-tree based on 28S ribosomal RNA gene, including the G. galapagoensis identified in this report, highlighted in bold. The branch numbers represent the ultrafast bootstrap support.

opencc-zeroDec 2023View details →

Characterization files for the analysis of Mg-Zn nanoferrites flavonoids

Nanosized ferrites MgxZn1-xFe2O4 (0 < x <1) was effectively synthesized using a wet ferritization method. The obtained spinel nanoparticles were then treated with flavonoids (Flv) extracted from agricultural waste of Punica granatum L. and Allium cepa L. Various characterization techniques such as FTIR, XRD, DTA-TGA, VSM, FE-SEM, TEM, EDX, and BET were utilized to analyze the surface morphology, magnetic properties, and elemental composition. The X-ray diffractograms revealed that the synthesized MgxZn1-xFe2O4 (MZFO) nanoparticles displayed a uniform cubic spinel structure, indicating the presence of a single phase. Morphological analysis revealed two distinct categories of MZFO nanoparticles: flower-shaped and plate-shaped particles. The attendance of Mg, Zn, O, Fe, and C elements in both MZFO and Flv/MZFO samples was confirmed by EDX analysis. TEM analysis further confirmed that each particle of the modified MZFO sample was a single crystal with an average particle size of 22 nm. Additionally, the modified MZFO nanoparticles exhibited a weight loss of 39.17% due to surface modification. Notably, the modified MZFO nanoparticles displayed remarkable superparamagnetic behavior with a saturation magnetization of up to 41.875 emu.g-1. BET analysis demonstrated that the Flv/MZFO nanoparticles possessed a mesoporous structure with a total pore volume of 0.1349 cm3/g, an average pore size of 17.044 nm, and a specific surface area of 31.655 m2/g. The conjugated Flv/MZFO nanoferrites exhibited significant antibacterial efficacy, with inhibition zones of 7 mm and 8 mm against Gram-positive and Gram-negative bacteria, respectively.

opencc-by-4.0Dec 2023View details →

Global Regionalized Characterization Factors for Phosphorus and Nitrogen Impacts on Freshwater Fish Biodiversity

Overview and guidance for using the data in "CFs_freshwater_eutrophication" related to the article "Global Regionalized Characterization Factors for Phosphorus and Nitrogen Impacts on Freshwater Fish Biodiversity"   See the "readme_CFs_freshwater_eutrophication.pdf" file to find the details of the enclosed data.   Units <ul> <li>Phosphorus from direct emissions to freshwater or diffuse sources on the soil: PDF·year/kgP</li> <li>Nitrogen from direct emissions to freshwater or diffuse sources on the soil: PDF·year/kgN</li> <li>Erosion: PDF·year/(m2·year)</li> </ul> Please excuse any typos in the units in the xlsx files.

opencc-zeroDec 2023View details →

Characterizing contemporary evolutionary change in a recently isolated population of Threespine Stickleback (Gasterosteus aculeatus L.)

Parallel evolution of lateral plates and body shape in threespine stickleback (Gasterosteus aculeatus) is an iconic example of adaptation. We test a case of contemporary evolutionary transition in a recently isolated population of marine G. aculeatus in British Columbia, Canada. We investigate Ectodysplasin (Eda) genotypes, plate counts, neutral genetic divergence and whole-body phenotypes to determine genetic and phenotypic distance between this population and nearby comparative populations. Our focal population is in the process of adapting both genetically and phenotypically to a freshwater environment and we provide an example of the genetic basis for parallel evolutionon a contemporary timescale. The frequency of Eda genotypes and lateral plate phenotypes in our focal population are not consistent with those of marine or fully freshwater populations. Although our focal population is genetically distinct from nearby marine populations, these fish still more closely resemble marine populations in overall body shape while demonstrating an intriguing intermediate phenotype. Eda frequency and lateral plate phenotype change faster than body shape in response to freshwater conditions, suggesting that the pace of adaptation differs across traits in response to the same environmental conditions. Our results further bolster the case for G. aculeatus as a key model of contemporary evolution.