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Fig. 57 in The Southeast Asian Pholcus halabala species group (Araneae, Pholcidae): new data from field observations and ultrastructure
Fig. 57. Known distributions of species tentatively assigned to the Pholcus halabala species group.
Fig. 17 in The Southeast Asian Pholcus halabala species group (Araneae, Pholcidae): new data from field observations and ultrastructure
Fig. 17. Known distribution of the core group of the Pholcus halabala species group.
Fig. 110 in The Southeast Asian Pholcus halabala species group (Araneae, Pholcidae): new data from field observations and ultrastructure
Fig. 110. Known distribution of the Pholcus krabi species group.
Data for [Rock magnetism of quartz and feldspars chemically separated from pelagic red clay: a new approach to provenance study]
<p>MPMS and XRD data used in the manuscript Rock magnetism of quartz and feldspars chemically separated from pelagic red clay: a new approach to provenance study.</p>
Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce
<p>This dataset includes files and scripts used for the paper "Genomic data provides new insights on the demographic history and the extent of recent material transfers in Norway spruce". </p>
Neotropical leaf-litter beetle genus Motonerus (Coleoptera: Hydrophilidae): new species, distribution data and description of third instar larva
<p>Numerous new material of the genus <em>Motonerus </em>Hansen, 1989 (Coleoptera: Hydrophilidae: Sphaeridiinae) was examined over the past decade, resulting in the discovery of several undescribed species as well as new distributional records for most of the previously described species. Three species are here described as new: <em>Motonerus explanatus </em>sp. nov. (Panama), <em>M. inca </em>sp. nov. (Venezuela, Ecuador, Peru, Bolivia) and <em>M. sofiae </em>sp. nov. (Peru). New country records are provided for <em>M. depressus </em>Fikáček & Short (new for Venezuela, Ecuador, Peru and Bolivia), <em>M. hanseni </em>Fikáček & Short (new for Panama) and <em>M. problematicus </em>Fikáček & Short (new for Panama). An updated identification key and distributional maps are provided for all species, along with complete occurrence data in a DarwinCore formatted file. Potential distribution of the genus is modelled using the maximum entropy approach. Wing morphology is examined in detail, which revealed most species are macropterous, with <em>M. andersoni </em>Fikáček & Short being brachypterous, and <em>M. apterus </em>Fikáček & Short, <em>M. oosternoides </em>Fikáček & Short and <em>M. explanatus </em>sp. nov. micropterous. The third instar of the putative larva of <em>M. obscurus </em>Hansen is briefly described based on larvae collected in association with adults.</p>
Experimental data and benchmarks used in the paper "Nucleosome Dynamics: A new tool for the dynamic analysis of nucleosome positioning"
<p>Experimental data used to illustrate the analysis with Nucleosome Dynamics pipeline. Three publicly available data sets were used:</p> <ol> <li> <p>Yeast metabolic cycle MNase-seq data downloaded from GEO under accession number GSE77631 corresponding to time points 9 and 12<br> Nocetti, N., and Whitehouse, I. (2016). Nucleosome repositioning underlies dynamic gene expression. Genes & Development 30, 660–672.</p> </li> <li> <p>MNase-seq data for S. cerevisiae cells synchronized in G1 and S phase, as described by Deniz (2016). Raw data available under accession number SAMEA2698380<br> Deniz, Ö., Flores, O., Aldea, M., Soler-López, M., and Orozco, M. (2016). Nucleosome architecture throughout the cell cycle. Scientific Reports 6, 19729.</p> </li> <li> <p>MNase-seq data for S. cerevisiae grown in different media: YPD, Gal, and EtOH. Data aligned to sacCer1 downloaded from GEO using accession numbers GSM351492, GSM351493, and GSM351494.</p> Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ et al. The DNA-encoded nucleosome organization of a eukaryotic genome. <em>Nature</em> 2009 Mar 19;458(7236):362-6. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19092803">19092803</a></li> </ol> <p>Each tar file contains two folders:</p> <ul> <li>inputs: bam/RData files can be used to run Nucleosome Dynamics analyses. bigWig files contain nucleosome coverage and can be used to visualise in a genome browser. </li> <li>outputs: results from all analyses (nucleR, NFR, TSS, Periodicity, Stiffness, NucDyn)</li> </ul> <p> </p> <p>Simulated data used to benchmark nucleosome positioning by nucleR, and nucleosome dynamics by NucDyn, DANPOS and Dimnp.</p> <p><strong>Figure </strong><strong>2B: </strong>synthetic data simulated for comparison of nucleR and Danpos to detect a second family of nucleosomes. Each folder pX contains simulations when the second nucleosome is present in X% of the families.</p> <p><strong>Figure 2C</strong>: Distance between the dyads identified by nucleR and DANPOS to the dyad position in the true synthetic nucleosome map for fuzzy and well positioned nucleosomes.</p> <p><strong>Figure 2D</strong>: Synthetic data used to compute sensitivity of the EVICTION prediction for NucDyn, DANPOS and Dimnp. Evictions were simulated removing reads from a given percentage of families (10%, 20%, …, 90%) and were identified from DANPOS output as a nucleosome with point_log2FC < -1 and point_diff_FDR < 0.01 (point with highest difference in the two samples, as reported by the software), and with default parameters for Dimnp </p> <p><strong>Figure 2E</strong>: Synthetic data used to compute sensitivity of the SHIFT prediction. Shifts were introduced displacing reads from 1 to 5 DNA turns (i.e. 10-50 bp) and modifying different percentages of the families (10%, 20%, …, 90%). </p> <p>For each simulated data:</p> <ul> <li><em> *.RData</em> files can be used to run nucleR or NucDyn (*mod* corresponds to the modified reads: eviction or shift introduced)</li> <li><em>*.bed </em>files can be used to run DANPOS or Dimnp (*mod* corresponds to the modified reads: eviction introduced)</li> <li>results/ folder contains results from DANPOS</li> <li><em>NR.gff</em> contains the results from nucleR (*mod* corresponds to the results for modified reads: eviction or shift introduced)</li> <li><em>ND.gff</em> contains the results from NucDyn</li> <li><em>res_dimnp_*</em> contains the results from Dimnp</li> </ul> <p><strong>FigSupDanposShift:</strong> Synthetic data used to compute sensitivity of the SHIFT prediction for DANPOS. Shifts were introduced displacing reads from 1 to 5 DNA turns (i.e. 10-50 bp) and modifying different percentages of the families (10%, 20%, …, 90%) and were identified from DANPOS output as a nucleosome with treat2control_dis-10 larger than the given displacement and point_diff_FDR < 0.01 (point with highest difference in the two samples, as reported by the software).</p> <p>For each simulated data:</p> <ul> <li><em> *.bed</em> files contain the modified nucleosome positions</li> <li><em>results</em> folder contains output from DANPOS</li> </ul>
New Zealand native forest plant cover data for Popovic et al. MEE (2019), Untangling direct species associations from indirect mediator species effects with graphical models.
<p>Forest cover measurements were collected at 1246 native forest sites that form part of a network of permanent 20 x 20 m plots spread throughout New Zealand. A total of 1831 plant species were present in these plots, with the most common being herbs, graminoids, ferns, shrubs and trees. Plant cover (in ordinal categories) was assessed for each species in several tiers at different heights. The cover data we analysed (<em>NZ_native_forest_cover.csv) </em>were the maximum cover recorded over all the tiers at the 964 sites identified as native forests, containing 1311 species with at least one presence. <em>NZ_native_forest_species.csv</em> contains species data including species name, exotic/native, and plant type (tree, shrub, etc.), corresponding to the plant species in the columns of <em>NZ_native_forest_cover.csv</em>.</p> <p>We acknowledge the use of data drawn from the Natural Forest plot data collected between January 2002 and March 2007 by the LUCAS programme for the Ministry for the Environment, New Zealand.</p> <p> </p>
Fig. 9. t in Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae)
Fig. 9. t-SNE ordination of the combined morphology + geometric morphometrics data.
Fig. 8 in Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae)
Fig. 8. Ordination from the principal component analysis of relative warps.
Fig. 1 in Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae)
Fig. 1. ML tree resulted from the analysis of concatenated ITS2 and rbcL sequences.
Fig. 4 in Mysterious chokeberries: new data on the diversity and phylogeny of Aronia Medik. (Rosaceae)
Fig. 4. ML tree from the LEAFY2 sequences.
Text-fig. 7. Amblypterus latus AGASSIZ, 1833. Reconstruction of the body, x 1.0, original. in New Data On The Osteology Of The Actinopterygian Fish Amblypterus And The Relationship Between Amblypterus And Paramblypterus
Text-fig. 7. Amblypterus latus AGASSIZ, 1833. Reconstruction of the body, x 1.0, original.
Fig. 19 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 19. Distribution of Ampedus tristis in Lithuania
Fig. 15 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 15. Distribution of Ampedus nigroflavus in Lithuania
Fig. 13 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 13. Distribution of Procraerus tibialis in Lithuania
Fig. 11 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 11. Distribution of Paraphothistus nigricornis in Lithuania
Fig. 12 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 12. Distribution of Calambus bipustulatus in Lithuania
Fig. 7 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 7. Distribution of Hypnoidus riparius in Lithuania
Fig. 5 in New data on little known species of click beetles (Coleoptera: Elateridae) in Lithuania
Fig. 5. Distribution of Cidnopus pilosus in Lithuania
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.