Find research datasets worth reusing

opencc-by-4.0Jan 2024View details →

WikiAligner alignments - 14 Jan 2024

The eighteen Excel documents included in this download have been produced by the WikiAligner tool, which is designed to highlight text in one language edition of Wikipedia that has been translated from another.

.bam alignment files of Illumina and ONT sequencing of pREF plasmid

The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides the first universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.

Aligning renewable energy expansion with climate-driven range shifts

Fossil fuel dependence can be reduced, in part, by renewable energy (RE) expansion. Increasingly, RE siting seeks to avoid significant impacts on biodiversity but rarely considers how species ranges will shift under climate change. Here, we undertake a systematic literature review on the topic and overlay future RE siting maps with the ranges of two threatened species under future climate scenarios to highlight this potential conflict.

Alignments of reindeer/caribou mitogenome sequences

Climate warming at the end of the last glacial period had profound effects on the distribution of cold-adapted species. As their range shifted towards northern latitudes, they were able to colonise previously glaciated areas, including remote Arctic islands. However, there is still uncertainty about their colonisation routes and timings. At the end of the last ice age, reindeer/caribou (Rangifer tarandus) expanded to the Holarctic region and colonised the archipelagos of Svalbard and Franz Josef Land. Earlier studies have proposed two possible colonisation routes, either from the Eurasian mainland or from Canada via Greenland. Here, we used 174 ancient, historical, and modern mitogenomes to reconstruct the phylogeny of reindeer across its whole range and to infer the colonisation route of the Arctic islands. Our data shows a close affinity among Svalbard, Franz Josef Land, and Novaya Zemlya reindeer. We also found tentative evidence for positive selection in the mitochondrial gene ND4, which is possibly associated with increased heat production. Our results thus support a colonisation of Arctic archipelagos from the Eurasian mainland and provide some insights into the evolutionary history and adaptation of the species to its High Arctic habitat.

Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies

Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17–20th centuries. Here we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.

opencc-by-4.0Feb 2024View details →

STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping

Spatial transcriptomics (ST) technologies enable high throughput gene expression characterization within thin tissue sections. However, comparing spatial observations across sections, samples, and technologies remains challenging. To address this challenge, we developed STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. We apply STalign to align ST datasets within and across technologies as well as to align ST datasets to a 3D common coordinate framework. We show that STalign achieves high gene expression and cell-type correspondence across matched spatial locations that is significantly improved over landmark-based affine alignments. Applying STalign to align ST datasets of the mouse brain to the 3D common coordinate framework from the Allen Brain Atlas, we highlight how STalign can be used to lift over brain region annotations and enable the interrogation of compositional heterogeneity across anatomical structures.  STalign is available as an open-source Python toolkit at <a href="https://github.com/JEFworks-Lab/STalign">https://github.com/JEFworks-Lab/STalign</a> and as supplementary software with additional documentation and tutorials available at <a href="https://jef.works/STalign">https://jef.works/STalign</a>. Here we have included alignment results that were used in performance analysis of STalign: We aligned Slice 2 Replicate 3 to Slice 2 Replicate 2 of the MERFISH mouse coronal brain sections available from Vizgen Data Release V1.0. May 2021 (<a href="https://info.vizgen.com/mouse-brain-map">https://info.vizgen.com/mouse-brain-map</a>). <ul> <li>STalign_S2R3_to_S2R2.csv.gz contains cell ids, original cell centroid positions of S2R3, cell positions of S2R3 after alignment to S2R2 with STalign, cell positions of S2R3 after supervised affine alignment to S2R2, and counts for genes and blanks.</li> <li>STalign_S2R2.csv.gz contains cell ids, cell centroid positions of S2R2 and counts for genes and blanks.</li> </ul> Additionally, we aligned Slice 2 Replicate 3 to a Visium dataset of an FFPE preserved adult mouse brain were obtained from the 10X Datasets website for Spatial Gene Expression Dataset by Space Ranger 1.3.0 (<a href="https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0">https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0</a>). <ul> <li>STalign_S2R3_to_Visium.csv.gz contains cell ids, original cell centroid positions of S2R3, cell positions of S2R3 after alignment to Visium H&E staining with STalign, and counts for genes and blanks.</li> </ul> Furthermore, we performed alignments with the 50um resolution 3D Allen Reference Atlas Nissl common coordinate framework, CCF  (<a href="https://help.brain-map.org/display/mouseconnectivity/API">https://help.brain-map.org/display/mouseconnectivity/API</a>). We applied STalign to align the Allen CCF to each of the 9 MERFISH slices (3 slice locations with 3 biological replicates) provided by Vizgen. Because the Allen CCF has annotated brain regions, we were able to lift over those brain region annotations to label all cells in the MERFISH datasets. Also, since the STalign mappings from the Allen CCF to the MERFISH slices are invertible, for each slice we can apply the inverse of the mapping to get cell positions in the Allen CCF coordinates. <ul> <li>STalign_SXRX_with_structure_id_name.csv.gz contains cell ids for Slice X Replicate X, original cell centroid positions, cell xyz-coordinates in Allen CCF, brain structure id per cell, brain structure acronym</li> </ul> To evaluate the 3D CCF alignment, we performed unified transcriptional clustering analysis and cell-type annotation. All MERFISH datasets were combined. Transcriptional clustering analysis and cell type annotation was performed using the SCANPY package [version 1.9.1]. Data were normalized to counts per million (scanpy: normalize_total) and log transformed (scanpy: log1p). PCA (scanpy: pca) was computed on the cell by gene matrix. A neighborhood graph of cells using the top 10 PCs and 10 nearest neighbors was created (scanpy: neighbors), and Leiden clustering was performed on this graph (scanpy: leiden) to identify 29 clusters. Differentially expressed genes were extracted from each cluster (scanpy: rank_genes_groups), and cell-types were annotated based on marker genes in each cluster. <ul> <li>STalign_celltypeannotations_merfishslices_v2.csv.gz contains for all nine slices cell ids and cell type annotations</li> </ul> This updated (v2) cell-type annotation file contains a new column with simplified cell-types. Briefly, we fixed typos, standardized lower case/upper case formats, merged subclasses of each cell-types. For example, subclasses of astrocytes, which are originally labeled as “Astrocytes”, “Astrocytes(1)”, “Astrocytes(2)”, “Astrocytes(3)”, are all labeled as “Astrocytes” in the added column. Note: Cell ids may have been mutated from original string of numbers through reading and writing across programming languages that handle numbers with different precision. If using R to read the files shared here, one can find the cells in STalign_celltypeannotations_merfishslices_v2.csv.gz that correspond with STalign_SXRX_with_structure_id_name.csv.gz when cell ids are formatted as a double in scientific notation, which is how R will read the file automatically.

Alignments and tree files from: Phylogenetic relationships within tribe Hibisceae (Malvaceae) reveal complex patterns of polyphyly in Hibiscus and Pavonia

The diverse and spectacular Hibisceae tribe comprises over 750 species. No studies, however, have broadly sampled across the dozens of genera in the tribe, leading to uncertainty in the relationships among genera. The non-monophyly of the genus Hibiscus is infamous and challenging, whereas the monophyly of most other genera in the tribe has yet to be assessed, including the large genus Pavonia. Here we significantly increase taxon sampling in the most complete phylogenetic study of the tribe to date. We assess monophyly of most currently recognized genera in the tribe and include three and thirteen newly sampled sections of Hibiscus and Pavonia, respectively. We also include five rarely sampled genera and 137 species previously unsampled. Our phylogenetic trees demonstrate that Hibiscus, as traditionally defined, encompasses at least 20 additional genera. The status of Pavonia emerges as comparable in complexity to Hibiscus. We offer clarity in the phylogenetic placement of several taxa of uncertain affinity (e.g., Helicteropsis, Hibiscadelphus, Jumelleanthus, and Wercklea). We also identify two new clades and elevate them to the generic rank with the recognition of two, new monotypic genera: 1) Blanchardia M.M.Hanes & R.L.Barrett is a surprising Caribbean lineage that is sister to the entire tribe, and 2) Astrohibiscus McLay & R.L.Barrett represents former members of Hibiscus caesius s.l. Cravenia McLay & R.L.Barrett is also described as a new genus for the Hibiscus panduriformis clade which is allied to Abelmoschus. Finally, we introduce a new classification for the tribe and clarify the boundaries of Hibiscus and Pavonia.

opencc-by-4.0Jan 2024View details →

The alignments of chloroplast genome sequences and nuclear ribosomal DNA fragments of six oak species sampled in the hot-dry valley of the Jinsha River, southwestern China

Both chloroplast (cp) genome sequences and nuclear ribosomal (nr) DNA were assembled using GetOrganelle v.1.7.6.1 for 18 oak trees sampled in the Panzhihua Cycad National Nature Reserve, Sichuan Province, China. These trees belong to six oak species, including Quercus cocciferoides, Q. dolicholepis, Q. franchetii, Q. griffithii, Q. longispica, and Q. variabilis. We used PhyloSuite v.1.1.152 to extract coding sequences (CDSs), tRNA genes, rRNA genes, introns, and intergenic spacers (IGSs) of the 18 oak cp genomes. These sequences were aligned separately using MAFFT v.7.3.13 and manually adjusted with BioEdit v.7.2.5. Length variations in mononucleotide repeats were excluded and inversions were replaced with their reverse complements because of their tendency for homoplasy. Other indels were coded as binary characters according to the simple gap coding method using GapCoder. Separate assignments were concatenated according to their respective positions in the cp genome to obtain the alignments of LSC, SSC, IRb, and the whole cp genome.

opencc-by-4.0Mar 2024View details →

Gene trees and corresponding nucleotide/protein alignments across 17 species (including 13 fishes)

This archive contains gene trees and corresponding nucleotide/protein alignments across 17 species (including 13 fishes).

opencc-by-4.0Dec 2023View details →

Aligning Data Management Plans with Community Standards using FAIR Implementation Profiles

Here you can find the files corresponding to our submission titled 'Aligning DMPs with Community Standards using FIPs'. - VU DMP template and the mapping is included in the folder /VU-DMP-template-and-mapping - All the FAIR Implementation Profiles are included in the folder /FIPs. - The knowledge model we created for the project, and a small demo of the interface are in the folder /KM-and-demo. - The folder /user-study consists of the following:   a) The mock DMPs we provided to the participants of this research are in /mock_DMPs.   b) We downloaded the resulting DMPs after participants completed their DMPs, they are in the folder /resulting_DMPs.   c) Survey results can be found in the folder /survey_results.   d) Some Python scripts were used for the analysis of the survey results. They are in the folder /Python_script_for_analysis. The project is open source under the license CC-BY 4.0. Contact: Shuai Wang (shuai.wang@vu.nl)

opencc-by-4.0Oct 2023View details →

Relative Contributions of Field-Aligned Currents and Particle Precipitation to the Inter-Hemispheric Asymmetry at High Latitudes During 2015 St. Patrick Day Storm

Data for Space Weather paper "Relative Contributions of Field-Aligned Currents and Particle Precipitation to the Inter-Hemispheric Asymmetry at High Latitudes During 2015 St. Patrick Day Storm".

opencc-zeroApr 2024View details →

Data rom: Stiffness anisotropy coordinates supracellular contractility driving long-range myotube-ECM alignment

The ability of cells to organize into tissues with proper structure and function requires the effective coordination of proliferation, migration, polarization, and differentiation across length scales. Skeletal muscle is innately anisotropic; however, few biomaterials can emulate mechanical anisotropy to determine its influence on tissue patterning without introducing confounding topography. Here, we demonstrate that substrate stiffness anisotropy coordinates contractility-driven collective cellular dynamics resulting in C2C12 myotube alignment over millimeter-scale distances. When cultured on mechanically anisotropic liquid crystalline polymer networks (LCNs) lacking topography, C2C12 myoblasts collectively polarize in the stiffest direction. Cellular coordination is amplified through reciprocal cell-ECM dynamics that emerge during fusion, driving global myotube-ECM ordering. Conversely, myotube alignment was restricted to small local domains with no directional preference on mechanically isotropic LCNs of the same chemical formulation. These findings provide valuable insights for designing biomaterials that mimic anisotropic microenvironments and underscore the significance of stiffness anisotropy in orchestrating tissue morphogenesis.

opencc-zeroNov 2024View details →

Dataset for P. Ripka, M. Mirzaei, J. Maier: Flat Magnetic X-Y Alignment sensor, IEEE Sensors Letters Vol. 8, Iss. 7, 2024, pp. 1-4 10.1109/LSENS.2024.3414375

Open the record for dataset details and reuse information.

opencc-by-4.0Jun 2022View details →

Alignments used for the phylogenies in "Caryophylliids (Anthozoa, Scleractinia) have a mitochondrial gene rearrangement: lesson learned from mitochondrial and nuclear phylogenomics"

"mitochondrial_caryotree.phy": concatenated alignment of mitochondrial data in phylip format; "mitochondrial_caryotree.partitions.txt": indication of start/stop positions of each partition in the mitochondrial data alignment; "nuclear_caryotree_55taxa-50p.phylip": alignment of nuclear exons and ultraconserved elements in phylip format.

opencc-by-4.0Sep 2021View details →

Where is Region 1 field-aligned current generated?

This contains the original simulation data used by the paper 'Where is Region 1 field-aligned current generated?', which will appear in Journal of Geophysical Research - Space Physics. The data were obtained by the global MHD simulation (REPPU) with Level 6.  The VTK file (Visualization Tookkit format) contains the physical variables in the magnetosphere at t = 244. 8 min as <ul> <li>plasma pressure (P in nPa),</li> <li>velocity vector (V in km/s),</li> <li>current density vector (J in nA/m2),</li> <li>magnetic field vector (B in nT).</li> </ul> The VTK file can be opened by Visualization Toolkit, and 3-D visualization software packages "VisIT", and "ParaView".    The ASCII files named packet-position-P.txt and packet-position-Q.txt include lists of the position of the packet traced backward in time from the positions P and Q, respectively.

opencc-by-4.0Dec 2021View details →

Data for: Correlated states in doubly-aligned hBN/graphene/hBN heterostructures

Interfacial moiré superlattice in van der Waals vertical assemblies effectively reconstructs the crystal symmetry, leading to opportunities for investigating exotic quantum states. Notably, a two-dimensional nanosheet has top and bottom open surfaces, allowing the specific case of doubly aligned super-moiré lattice to serve as a toy model for studying the tunable lattice symmetry and the complexity of related electronic structures. Here, we show that by doubly aligning a monolayered graphene to both top and bottom encapsulating hexagonal boron nitride (h-BN), multiple conductivity minima are observed away from the main Dirac point, which are sensitively tunable with respect to the small twist angles. Moreover, our experimental evidences together with theoretical calculations suggest correlated insulating states at integer fillings of -5, -6, -7 electrons per moiré unit cell, possibly due to inter-valley coherence. Our results provide a way to construct intriguing strong correlations in 2D electronic systems, in the weak interaction regime.

opencc-by-4.0Dec 2021View details →

Supplemental Material for Genome Editing in Crop Plant Research - Alignment of expectations and current developments

Supplemental Material for Paper "Genome Editing in Crop Plant Research - Alignment of expectations and current developments" as submitted to Plants

opencc-by-4.0Jan 2022View details →

Imputed Multiple Sequence Alignment used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'

Multiple Sequence Alignment of imputed SARS-CoV-2 sequences used in 'Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples'

opencc-by-4.0Jan 2022View details →

Utilizing Hydrothermal Processing to Align Structure and In Vitro Digestion Kinetics between Three Different Pulse Types

The data used for the graphs in the paper: Pälchen, K.; Van den Wouwer, B.; Duijsens, D.; Hendrickx, M.E.; Van Loey, A.; Grauwet, T. Utilizing Hydrothermal Processing to Align Structure and In Vitro Digestion Kinetics between Three Different Pulse Types. Foods 2021, 11, 206. https://doi.org/10.3390/foods11020206 Abstract Processing results in the transformation of pulses’ structural architecture. Consequently, digestion is anticipated to emerge from the combined effect of intrinsic (matrix-dependent) and extrinsic (processed-induced) factors. In this work, we aimed to investigate the interrelated effect of intrinsic and extrinsic factors on pulses’ structural architecture and resulting digestive consequences. Three commercially relevant pulses (chickpea, pea, black bean) were selected based on reported differences in macronutrient and cell wall composition. Starch and protein digestion kinetics of hydrothermally processed whole pulses were assessed along with microstructural and physicochemical characteristics and compared to the digestion behavior of individual cotyledon cells isolated thereof. Despite different rates of hardness decay upon hydrothermal processing, the pulses reached similar residual hardness values (40 N). Aligning the pulses at the level of this macrostructural property translated into similar microstructural characteristics after mechanical disintegration (isolated cotyledon cells) with comparable yields of cotyledon cells for all pulses (41–62%). We observed that processing to equivalent microstructural properties resulted in similar starch and protein digestion kinetics, regardless of the pulse type and (prolonged) processing times. This demonstrated the capacity of (residual) hardness as a food structuring parameter in pulses. Furthermore, we illustrated that the digestive behavior of isolated cotyledon cells was representative of the digestion behavior of corresponding whole pulses, opening up perspectives for the incorporation of complete hydrothermally processed pulses as food ingredients.