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1,199 results for “alignment”
Cross-phyla protein annotation by structural prediction and alignment
<p><strong>Background:</strong> Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer protein identity, however this approach loses predictive power at longer evolutionary distances. Here we propose a workflow for protein annotation using structural similarity, exploiting the fact that similar protein structures often reflect homology and are more conserved than protein sequences.</p> <p><strong>Results:</strong> We propose a workflow of openly available tools for the functional annotation of proteins via structural similarity (MorF: <strong>Mor</strong>pholog<strong>F</strong>inder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in >90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. We uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls.</p> <p><strong>Conclusions:</strong> Our work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.</p>
Trees and alignments for: A robust phylogenomic framework for the calamoid palms
<p>Target file, alignments, gene trees and species trees from phylogenomic analyses in Kuhnhäuser et al. (2021), A robust phylogenomic framework for the calamoid palms, Molecular Phylogenetics and Evolution. <a href="https://doi.org/10.1016/j.ympev.2020.107067">https://doi.org/10.1016/j.ympev.2020.107067</a>.</p> <p>Raw sequence data are deposited in the European Nucleotide Archive of the European Bioinformatics Institute (<a href="https://www.ebi.ac.uk/ena">https://www.ebi.ac.uk/ena</a>) under project number PRJEB40689. Scripts for all phylogenetic analyses are available at <a href="https://github.com/BenKuhnhaeuser/PhyloFrame">https://github.com/BenKuhnhaeuser/PhyloFrame</a>.</p>
cre_mtc_essen_ses_alignment_dlfm2023
<p>This archive contains data that goes with:</p><p>Peter van Kranenburg and Eoin Kearns. 2023. Cross-Corpus Melodic Similarity For Enriching Archival Collections. In Proceedings of Digital Libraries for Musicology Conference (DLfM). ACM, New York, NY, USA.</p><p>The data contains a full distance matrix, ranked lists, and lists of similar pairs of melodies across four melody collections: The Meertens Tune Collections MTC-FS-INST-2.0, the EsAC Folk Song Databases, the Ceol Rince na hÉireann collection, and The Session.</p>
Data supplement for "Alignment of scanning lidars in offshore wind farms" - Wind Energy Science Journal
<p>These data are supplements for the calculations of the methods from the article "Alignment of scanning lidars in offshore wind farms".<br> The data was used to produce the results from the publication and is intended to be used here as sample data for illustrative purposes.</p>
Alignments used in "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families"
<p>Alignments used in de Vries et al. (2021) "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families" published as</p> <p>(1) a pre-print: https://doi.org/10.1101/2021.05.27.445924</p> <p>(2) in Plant Journal (in press)</p>
Alignment between type of landmark in different sources and the concept in the spatial reference objects ontology
<p>The five datasets represent a manually alignment between the landmark type of five different datasets archived <a href="https://doi.org/10.5281/zenodo.6480986">here</a> and a common vocabulary extracted from an application ontology defined for mountain rescue purposes, named <a href="https://hamac.ign.fr/owa/redir.aspx?C=cjlWje9SCaYsVOTLbxbOoIBLZUCS56nVb248cRSMTEDSENDFzybaCA..&URL=http%3a%2f%2fchoucas.ign.fr%2fdoc%2fontologies%2foor.owl%2f">Ontology of landmarks</a> (OOR).</p> <p>Each file represents the alignment for features belonging to a data source with the same OOR ontology.</p> <p>For example, the type «bivouac» from camptocamp.org source is aligned with the uri <a href="http://purl.org/choucas.ign.fr/oor#abri">http://purl.org/choucas.ign.fr/oor#abri</a> of the corresponding class «Shelter » in the ontology of landmark. The alignments models can be considered as a ground truth data.</p> <p>The alignments results are obtained using an ontology application named <a href="http://choucas.ign.fr/doc/ontologies/index-fr.html">OOR</a>. These specific results are obtained using the version of OOR V1.0.1 which is an improved version and contains new concepts compared to the first release 1.0.0. The new version of OOR (i.e. 1.0.1) will be released by the end of May 31 2022. The new link will be added here.</p> <p>This archive is released for transparency and reproducibility purposes.</p>
Refinements for Bragg coherent X-ray diffraction imaging: Electron backscatter diffraction alignment and strain field computation
<p>Here we present the final crystal reconstructions and analysis scripts for the paper titled "Refinement for Bragg coherent X-ray diffraction imaging: Electron backscatter diffraction alignment and strain field computation" published in Journal of Applied Crystallography, 55, 2022. Please see the README file for more information.</p>
Beyond the passive–active dichotomy: aligning research with the intervention continuum framework of ecological restoration
<p>The dataset and R script file are associated with the publication, "Krishnan, A. and Osuri, A.M. (2022), Beyond the passive-active dichotomy: aligning research with the intervention continuum framework of ecological restoration. Restoration Ecology:e13828. https://doi.org/10.1111/rec.13828"</p> <p>Please refer to the readme.txt file for more information on the dataset and analyses.</p>
THCHS-30 - Aligned IPA transcriptions
<p>This upload contains aligned IPA transcriptions for the <a href="https://www.openslr.org/18/">THCHS-30 dataset from OpenSLR</a>. Thereby, punctuation is added, silence marked and duration markers for each phoneme are assigned. Furthermore, the silence on the beginning and ending of each file is marked.</p> <p>The words were transcribed using <a href="https://pypi.org/project/pypinyin/">pypinyin</a> (v0.47.1) via <a href="https://pypi.org/project/dict-from-pypinyin/">dict-from-pypinyin</a> (v0.0.1) and mapped to IPA using the <code>pinyin-ipa-map-TONE3-all.json</code> mapping <a href="https://zenodo.org/record/7525638">from here</a>. The alignment was done using <a href="https://zenodo.org/record/6796264">Montreal Forced Aligner</a> (v2.0.5) and the acoustic model <a href="https://mfa-models.readthedocs.io/en/latest/acoustic/Mandarin/Mandarin%20MFA%20acoustic%20model%20v2_0_0a.html">Mandarin MFA</a> (v2.0.0a).</p> <p>Phoneme duration markers:</p> <ul> <li><code>˘</code> -> [0, 20) percentile (speaker-wise), e.g., <code>a˥˩˘</code></li> <li>(none) -> [20, 80) percentile (speaker-wise), e.g., <code>a˥˩</code></li> <li><code>ˑ</code> -> [80, 90) percentile (speaker-wise), e.g., <code>a˥˩ˑ</code></li> <li><code>ː</code> -> [90, inf) percentile (speaker-wise), e.g., <code>a˥˩ː</code></li> </ul> <p>Thereby each phoneme (including tones) was considered on its own, i.e., phonemes with different tones were not considered together for the percentile calculation.</p> <p>Silence markers:</p> <ul> <li><code>SILX</code> -> silence at start/end of a recording (aligned on all tiers)</li> <li><code>SIL0</code> -> no silence</li> <li><code>SIL1</code> -> [0, 33.33333333) percentile of all silences (speaker-wise)</li> <li><code>SIL2</code> -> [33.33333333, 66.66666666) percentile of all silences (speaker-wise)</li> <li><code>SIL3</code> -> [66.66666666, inf) percentile of all silences (speaker-wise)</li> </ul> <p>Files:</p> <ul> <li><code>grids.zip</code> <ul> <li>contains TextGrids for all audio files containing three tiers <code>words</code>, <code>phonemes</code> and <code>transcription</code> <ul> <li><code>words</code> contains the aligned Chinese words</li> <li><code>phonemes</code> contains the IPA pronunciations including silence markers at start and end (<code>SILX</code>)</li> <li><code>transcription</code> contains unaligned phonemes including punctuation and word boundary labels (<code>SIL0</code>)</li> </ul> </li> <li>the folder structure is equal to one from the dataset</li> </ul> </li> <li><code>grids-sdp.zip</code> <ul> <li>same as <code>grids.zip</code> except the folder structure is the one from <a href="https://pypi.org/project/speech-dataset-parser/">speech-dataset-parser</a> (v0.0.4)</li> </ul> </li> <li><code>preview-start/middle/end.png</code> <ul> <li>preview of the first TextGrid from speaker <code>A2</code> opened in Praat in different positions</li> </ul> </li> <li><code>words-vocabulary.txt</code> <ul> <li>contains all Chinese words from tier <code>words</code></li> </ul> </li> <li><code>phonemes-vocabulary.txt</code> <ul> <li>contains all phonemes from tier <code>phonemes</code></li> </ul> </li> <li><code>transcription-vocabulary.txt</code> <ul> <li>contains all phonemes/punctuation from tier <code>transcription</code></li> </ul> </li> <li><code>phonemes-durations.pdf</code> <ul> <li>contains the plotted phoneme duration distribution of tier <code>phonemes</code></li> </ul> </li> <li><code>phonemes-durations-simple.pdf</code> <ul> <li>contains the plotted phoneme duration distribution of tier <code>phonemes</code> if all duration markers are ignored</li> </ul> </li> <li><code>phonemes-durations-simple-toneless.pdf</code> <ul> <li>contains the plotted phoneme duration distribution of tier <code>phonemes</code> if all duration markers and tones are ignored</li> </ul> </li> <li><code>pronunciations-broad.dict</code> <ul> <li>contains the broad pronunciations for each word including punctuation but not duration markers</li> <li>e.g., <code>一下。 i˥ ɕ j a˥˩ 。</code></li> </ul> </li> <li><code>pronunciations-narrow.dict</code> <ul> <li>contains the narrow pronunciations for each word including punctuation, duration markers and weights (= occurrence) over all speakers</li> <li>e.g., <code>一下。 3 i˥ ɕ j a˥˩ː 。</code></li> </ul> </li> <li><code>pronunciations-narrow-speakers.zip</code> <ul> <li>contains the narrow pronunciations separated for each speaker</li> </ul> </li> <li><code>script.sh</code> <ul> <li>contains the script to reproduce all results</li> <li>error in line 32: replace with <code>speech-dataset-parser==0.0.4</code></li> </ul> </li> </ul>
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Catalog of Coronal Mass Ejections Observed in Conjunction between Radially Aligned Spacecraft in the Inner Heliosphere
<p>This catalog lists 47 CME events observed in a longitudinal conjunction between MESSENGER, Venus Express, STEREO, and Wind/ACE. We list the onset date and time of the probable CME candidate. If the CME was observed by LASCO onboard the SOHO<br> spacecraft, we report the average CME onset time as calculated in the CDAW catalog (average between first-order-constant speed and second-order-constant acceleration onset times). Otherwise, we report the time of the first STEREO/COR image containing the<br> CME. We then list the arrival times of the shock/discontinuity, magnetic ejecta leading edge and trailing edge at spacecraft 1 and 2. Arrival times at MESSENGER are listed from Winslow et al. (2015, 2017), Venus Express from Good and Forsyth (2016), STEREO from Jian, Russell, Luhmann, and Galvin (2018), and L1 from Richardson and Cane (2010). We also list the heliocentric distances of the spacecraft at the CME onset time, the longitudinal separation between the spacecraft when the discontinuity/ejecta arrives<br> at spacecraft 1, and the maximum magnetic field strength observed in the CME (including both the sheath and the ejecta) at each spacecraft. The maximum magnetic field strength measured in the CME at MESSENGER are listed from Winslow et al. (2015, 2017), the maximum magnetic field strength measured in the ejecta at Venus Express are listed from Good and Forsyth (2016). The longitudinal separations are in Heliographic Inertial (HGI) coordinates. We also list the initial CME speed. For the speed, we select the coronagraph which observed the CME closest to a limb event. Limb views signicantly minimize projection effects as compared to halo views and provide a better estimate of CME speeds. When LASCO observed the CME as a limb event, we report the second-order CME speed at 20 Rs (solar radius) listed in the CDAW catalog. For STEREO observations, we report the maximum<br> speed as listed in the CACTus catalog. We also list the average impact speeds at spacecraft 1 from the DBM (Vrsnak et al., 2013) and either the average impact speeds (when spacecraft 2 is Venus Express) or the maximum CME speed (when spacecraft 2 is<br> STEREO/Wind/ACE) measured at spacecraft 2. The maximum CME speeds measured at STEREO are listed from Jian et al. (2018) and at L1 listed from Richardson and Cane. (2010). We list the average transit speeds as well between the Sun and spacecraft 1,<br> spacecraft 1 and spacecraft 2, and the Sun and spacecraft 2.</p>
Multiple alignment of DNA-B sequences from CMMGV, EACMCV, EACMV, EACMKV, EACMMV, EACMZV, SACMV (7 "species")
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Multiple alignment of ACMV and ACMBFV DNA-B sequences
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Supporting Data: Complementary Organic Logic Gates on Plastic Formed by Self-Aligned Transistors with Gravure and Inkjet Printed Dielectric and Semiconductors
<p>The file contains the supporting data for the publication:</p> <p>S.G. Higgins, B.V.O. Muir, G. Dell'Erba, A. Perinot, M. Caironi, A.J. Campbell. Complementary Organic Logic Gates on Plastic Formed by Self-Aligned Transistors with Gravure and Inkjet Printed Dielectric and Semiconductors. doi: 10.1002/aelm.201500272. <em>Advanced Electronic Materials </em>(2015)</p> <p>See 'README.txt' for a description of the contents of the compressed file.</p>
Supporting Data: Self-Aligned Organic Field-Effect Transistors on Plastic with Picofarad Overlap Capacitances and Megahertz Operating Frequencies
<p>The file contains the supporting data for the publication:</p> <p>S.G. Higgins, B.V.O. Muir, G. Dell'Erba, A. Perinot, M. Caironi, A.J. Campbell. Self-Aligned Organic Field-Effect Transistors on Plastic with Picofarad Overlap Capacitances and Megahertz Operating Frequencies. doi: 10.1063/1.4939045. <em>Applied Physics Letters</em> (2016)</p> <p>See 'README.txt' for a description of the contents of the compressed file.</p>
Protein and DNA alignments for ILS and Entropy calculations
<p>Datasets for reproducing the Entropy and ILS calculations of the 3rd Chapter of my PhD.</p><p>Data include Protein, Exon and Intron alignments for 12 genes.</p>
Datasets of sequences, alignments and structural models generated for the structural prediction of complexes mediated by intrinsically disordered regions.
<p>This repository contains input and ouput files used and generated for the scanning of intrinsically disordered region and the prediction of their binding sites to receptor proteins using the <a href="https://github.com/i2bc/SCAN_IDR">SCAN_IDR</a> pipeline with AlphaFold2-Multimer.</p><p>It contains two archives: </p><ol><li><a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> dedicated to the analysis of a dataset of 42 protein complexes non redundant with the dataset used for AlphaFold2 training,</li><li><a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> dedicated to the analysis of 923 complexes from the ELM database.</li></ol><p>These data can be used to rerun specific sections of the pipeline and scripts provided in: <a href="https://github.com/i2bc/SCAN_IDR">https://github.com/i2bc/SCAN_IDR</a></p><h4><strong>Dataset of 42 non redundant complexes</strong></h4><p>The first archive <a href="https://zenodo.org/api/records/10068949/draft/files/scanidr_data_repository_corr6J08.tar/content"><i><strong>scanidr_data_repository_corr6J08.tar</strong></i></a> contains 3 compressed directories and a README file detailing their contents :</p><ul><li>the initial raw sequence and alignment data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the input and output data of every Alphafold run for every complex -> DIRECTORY <strong>af2_runs/</strong></li><li>the native reference structures -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p>The protein-peptide complex cases have been assigned a distinct index number, from 1 to 42, consistent across the several directories of the archive. Their corresponding directories are labelled as <i><index>_<pdbcode></i>.</p><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.2</i></p><h4><strong>Dataset of 923 complexes selected from the ELM database</strong></h4><p>The second archive <a href="https://zenodo.org/api/records/10068949/draft/files/923_elm_cases_repository.tar.gz/content"><i><strong>923_elm_cases_repository.tar.gz</strong></i></a> contains input and ouput files used and generated for the analysis of 923 Eukaryotic Linear Motifs (ELM) database entries.</p><p>Each ELM entry is indexed with specific integer id and is composed of a receptor and a ligand protein. </p><p>The archive contains a Table associating ELM indexes with the ELM entry information, 5 directories and a README file detailing their contents:</p><ul><li>the table describing ELM entries -> FILE <strong>Table_923ELM_uid_delimitations_info_for_archive.txt</strong></li><li>the initial raw sequence and multiple sequence alignment (MSA) data for every chain -> DIRECTORY <strong>fasta_msa/</strong></li><li>the concatenated MSA model for every ELM complex and protocol used -> DIRECTORY <strong>af2_elm_coali_inputs/</strong></li><li>the best model of every AF2 protocol for every complex according to the AF2 -> DIRECTORY <strong>af2_elm_models/</strong></li><li>the best model cut in the ligand part to select only the ELM motifs as used for the evaluation of the models -> DIRECTORY <strong>elm_cut_models/</strong></li><li>the reference structures used for the evaluation of the models -> DIRECTORY <strong>ref_capri_curated/</strong></li></ul><p><i>The models in this archive were generated using AlphaFold2-Multimer v2.3</i></p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the eastern Andean slopes and the biogeographic history of the genus"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of Torrent Treefrogs (Anura: Hylidae) of the Hyloscirtus bogotensis group from the Amazon foothills and the biogeographic history of the genus"</p> <p>The matrix is in NEXUS format and has 3259 bp and 25 terminals.</p> <p>Partitions are as follows:</p> <div>charset 12S = 1-955;</div> <div>charset ND1_nonCoding1 = 956-1279;</div> <div>charset ND1_Pos1 = 1280-2240\3;</div> <div>charset ND1_Pos2 = 1281-2241\3;</div> <div>charset ND1_Pos3 = 1282-2242\3;</div> <div>charset ND1_nonCoding2 = 2243-2361;</div> <div>charset cmyc_Pos1 = 2362-2779\3;</div> <div>charset cmyc_Pos2 = 2363-2780\3;</div> <div>charset cmyc_Pos3 = 2364-2781\3;</div> <div>charset Rag1_Pos1 = 2782-3415\3;</div> <div>charset Rag1_Pos2 = 2783-3416\3;</div> <div>charset Rag1_Pos3 = 2784-3417\3;</div>
Polarized, color-selective and semi-transparent organic photodiode of aligned merocyanine H-aggregates
<p>Data to report <a href="https://doi.org/10.1039/D4TC00678J">https://doi.org/10.1039/D4TC00678J</a>:</p> <p><span><span>Highly anisotropic thin films of H-type coupled dipolar merocyanines </span></span><span><span>with large dichroic ratios of over 50 </span></span><span><span>were </span></span><span><span>deposited by solution shearing. These layers were incorporated into simultaneously color- and polarization-selective organic photodiodes. Using a transparent non-fullerene acceptor, polarization-sensitive planar-heterojunction devices with an average visible transmittance of 93% were obtained.</span></span></p> <p> </p>
Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment
<p><a name="_Hlk158643946"></a><strong>Data description: Deprivation of loading during early healing of rat Achilles tendons affects extracellular matrix composition and structure, and reduces cell density and cell alignment</strong></p> <p><em>Malin Hammerman, Maria Pierantoni, Hanna Isaksson<sup> *</sup>, Pernilla Eliasson <sup>*</sup></em></p> <p><em><sup>* </sup></em><em>joint<sup> </sup>last authors</em></p> <p>This dataset contains microscope images obtained from sections of healing and intact rat Achilles tendons undergoing different in vivo loading protocols and different time points post-transection. The data presented are the full resolution microscope images available in lower resolution in the accompanying manuscript’s Supplementary Figures 4-6.</p> <p>Each zipped folders contain images (tif-files) from all time-points for each respective staining and loading group. </p> <ul> <li>Col1: Sections stained with Collagen 1 antibodies</li> <li>Col3: Sections stained with Collagen 3 antibodies</li> <li>Elastin: Sections stained with Elastin antibodies</li> <li>Full_loading: Free cage activity</li> <li>Reduced_loading: Paralysis of the calf muscle with Botox</li> <li>Minimal_loading: Botox combined with joint fixation using a steel-orthosis</li> <li>Intact_reference: Contralateral uninjured Achilles tendons, used as reference</li> </ul> <p>More description of the datasets inside the zipped files are available below and in the file 'Data Description.pdf'</p> <p> </p> <p><strong>Brief re-cap of methods</strong></p> <p>Histological analysis was performed on healing Achilles tendons from Female Sprague-Dawley rats, specific-pathogen free (11-12 weeks, weight 299 ± 15 g), that had undergone full transection [13] of the right Achilles tendon, and been exposed to different levels of loading. Altered loading was imposed through two mechanisms. Reduced loading involved intramuscular Botox injections in the right calf muscles to induce plantar flexor muscle paralysis [24]. Additionally, the rats in the minimal loading group received a steel-orthosis around their right hindlimb directly after surgery [24].</p> <p>Snap frozen tendons in OCT were sectioned longitudinally (7 μm thickness) and stained with immunofluorescent staining for collagen 1, collagen 3, or elastin. Sections were counterstained with DAPI followed by mounting. The tissue sections were imaged under a microscope (DMi8, Leica Microsystems, Wetzlar, Germany, with a Hamamatsu Orca LT Flash sCMOS camera) where fluorescence was detected at 550 nm (secondary antibody Alexa Fluor 594), 470 nm (secondary antibody Alexa Fluor 488) and 385 nm (DAPI), and exposure time was held constant for each color channel regarding magnification and staining.</p> <p>Mapping images of the entire tendon were obtained for one section per group (n=1 per healing time, loading group and ECM matrix protein). All images were adjusted to the negative control, where the primary antibody was omitted, to correct for unspecific antibody detection.</p> <p><strong>Microscope images and description of file-names </strong></p> <p>All data is presented in the form of .tif files. Please refer to the scale bars in the images. All image-files are named using the following abbreviations, as described below. As an example, the file name “Tendon_col1_FL_1W_col1.tif” refers to a tendon section stained for collagen 1 from a rat exposed to full loading for a period of 1 week after tendon transection, where only the channel for collagen 1 is shown, whereas “Tendon_col1_FL_1W_merged.tif” includes the channels for both staining for collagen 1 and DAPI of the same section.</p> <p>Col1: Sections stained with Collagen 1 antibodies<br>Col3: Sections stained with Collagen 3 antibodies<br>Elastin: Sections stained with Elastin antibodies<br>dapi: Sections stained with 4',6-Diamidino-2-Phenylindole Dihydrochloride.<br>FL: Full loading (free cage activity),<br>RL: Reduced loading (paralysis of the calf muscle with Botox),<br>ML: Minimal loading (Botox combined with joint fixation using a steel-orthosis)<br>IT: Intact contralateral Achilles tendons, used as reference.</p> <p>1W: Healing time point 1 week after transection<br>2W: Healing time point 2 weeks after transection<br>3W: Healing time point 3 weeks after transection<br>20W: Healing time point 20 weeks after transection</p> <p><strong>Settings for brightness and contrast</strong></p> <p><em>Collagen 1</em><br>1w FL 2000-12 000, UL 4000-10 000, ML 4000-12 000<br>2w FL 2500-10 000, UL 4000-10 000, ML 5000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 3000-11 000<br>IT 2000-8 000</p> <p>Collagen 3<br>1w FL 3000-12 000, UL 4000-10 000, ML 4000-13 000<br>2w FL 2000 - 7 000, UL 2500-12 000, ML 2000-12 000<br>3w FL 2000-12 000, UL 3500-13 000, ML 3500-14 000<br>12w FL 3000-12 000<br>20w FL 2000-12 000<br>IT 3000-12 000</p> <p>Elastin<br>1w FL 4000-10 000, UL 5000 - 8000, ML 3500-12 000<br>2w FL 3000-12 000, UL 3000-12 000, ML 3000-12 000<br>3w FL 2500-12 000, UL 2000-12 000, ML 2500-12 000,<br>12w FL 3500-12 000<br>20w FL 3500-12 000<br>IT 2000-12 000</p>
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.