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2,439 results for “Assembly”
BBS phase 1 & phase 2 high quality E. coli bin assembled genomes
<p>1,402 <em>Escherichia coli</em> bin assembled genomes derived from the metagenome data collected as part of the <a href="https://www.ucl.ac.uk/global-health/research/a-z/baby-biome-study">BabyBiome study (BBS)</a> phase 1 & phase 2.</p> <p>The data in this upload was first published as part of "<em>Group 2 and 3 ABC-transporter dependant K-antigen loci contribute significantly to variation in the invasive potential of Escherichia coli"</em> (Gladstone et al. 2024, to be released).</p> <h2>Files</h2> <p>Assembly data:</p> <ul> <li>BBS_E_coli_BAGs.tar: Archive containing sequences of the 1,402 bin assembled genomes.</li> <li>BBS_E_coli_metadata.tsv: Table linking the sequence assemblies to the subject data.</li> </ul> <p>Capsule predictions:</p> <ul> <li>BBS_E_coli_Kaptive_output.csv: Capsule predictions for all sequence data.</li> <li>BBS_E_coli_deduplicated_sequences_IDs.txt: Filenames for assemblies that constitute the 873 deduplicated sequences analysed in Gladstone et al. 2024.</li> </ul> <p>Quality control data:</p> <ul> <li>BBS_E_coli_demix_check_scores.tsv: Output from demix_check for the sequence assemblies.</li> <li>BBS_E_coli_checkm_results.tsv: Output from checkm.</li> <li>BBS_E_coli_gunc_results.tsv: Output from gunc.</li> </ul> <h2>Methods</h2> <h3>Bin assembled genomes</h3> <p>Source data:</p> <ul> <li>BBS phase 1: <a href="https://doi.org/10.1038/s41586-019-1560-1">Shao et al. 2019</a></li> <li>BBS phase 2: <a href="https://doi.org/10.1038/s41564-024-01804-9">Shao et al. 2024</a></li> </ul> <p>The data was produced using the mSWEEP and mGEMS pipeline (<a href="https://doi.org/10.12688/wellcomeopenres.15639.2">Mäklin et al. 2020</a> & <a href="https://doi.org/10.1099/mgen.0.000691">Mäklin et al. 2021</a>) following the steps described in <a href="https://doi.org/10.1038/s41467-024-49591-5">Khawaja, Mäklin, Kallonen, et al. 2024</a>.</p> <h3>Quality control</h3> <p>The BAGs in this upload were filtered with demix_check (<a href="https://github.com/harry-thorpe/demix_check">https://github.com/harry-thorpe/demix_check</a>) and only those with a quality score 1 or 2 are included. For the capsule type annotations, contigs shorter than 5,000bp were removed but the short contigs are still present in the uploaded files). Further QC data is available from checkm (<a href="https://genome.cshlp.org/content/25/7/1043.short">Parks et al. 2015</a>) and gunc (<a href="https://link.springer.com/article/10.1186/s13059-021-02393-0">Orakov et al. 2022</a>) results.</p> <h3>Multilocus sequence typing</h3> <p>Sequence type (ST) was determined using fastmlst (<a href="https://journals.sagepub.com/doi/10.1177/11779322211059238">Guerrero-Araya et al. 2021</a>) with the `ecoli#1` database.</p> <h3>PopPUNK clustering</h3> <p>Sequence clusters (SC) correspond to the database available from <a href="https://zenodo.org/records/12528310">https://zenodo.org/records/12528310</a> and were created using PopPUNK (<a href="https://genome.cshlp.org/content/29/2/304.short">Lees et al. 2019</a>). Construction is described in <a href="https://doi.org/10.1038/s41467-024-49591-5">Khawaja, Mäklin, Kallonen, et al. 2024</a>.</p> <h3>Capsule type annotations</h3> <p>The capsule type annotations were created using Kaptive (<a href="https://doi.org/10.1099/mgen.0.000800">Lam et al. 2022</a>) with an <em>E. coli</em> specific database available from <a href="https://github.com/rgladstone/EC-K-typing">https://github.com/rgladstone/EC-K-typing</a> and described in Gladstone et al. 2024.</p>
Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system
<p><em>Schistosoma mansoni </em>has a diploid genome of approximately 380 MB, organized in 7 pairs of autosomes and 2 sex chromosomes. The original <em>Schistosoma mansoni </em>Genome Project was completed by the Wellcome Sanger Institute in collaboration with The Institute for Genome Research using a Whole Genome Shotgun sequencing strategy. The draft assembly was subsequently improved first by incorporating Illumina reads from a clonal (single-miracidial) infection and more recently by incorporating long PacBio reads, HiC, and optical mapping data.</p> <p>Associated manuscript can be found at https://www.biorxiv.org/content/10.1101/2021.08.13.456314v1</p>
The effect of solvent on convectively-driven silica particle assembly: Decoupling surface tension,viscosity, and evaporation rate
<p>Dataset associated with 'The effect of solvent on convectively-driven silica particle assembly: Decoupling surface tension, viscosity, and evaporation rate’.</p> <p>The data is based on the figures below, published in the linked article (see the doi).</p> <p><strong>- Figure 1. S</strong>egmented and raw images of dip-coated films. <strong>(images, .TIF)</strong></p> <p><strong>- Figure 2. </strong>Calculated surface coverages <strong>(data, .csv)</strong></p> <p><strong>- Figure 3. </strong>Rheology on SiO<sub>2</sub>-iPrOH-Glycerol mixtures & SEM micrographs of particle films. <strong>(data, .csv; images, .TIF)</strong></p> <p><strong>- Figure 4. </strong>SEM micrographs of silica helices films. <strong>(images, .TIF)</strong></p> <p><strong>- Figure S1. </strong>Measured evaporated masses of each solvent as a function of time. <strong>(data, .csv)</strong></p> <p><strong>- Figure S2. </strong>TEM micrographs of SiO2 seeds and measured particle diameters. <strong>(data, .csv; images, .TIF)</strong></p> <p><strong>- Figure S3. </strong>TEM micrographs of SiO particles and measured particle diameters. <strong>(data, .csv; images, .TIF)</strong></p> <p><strong>- Figure S4. </strong>Calculated solvent fractions as a function of time. <strong>(data, .csv)</strong></p> <p><strong>- Figure S5.</strong> Rheology of i-PrOH-glycerol mixtures.<strong> (data, .csv)</strong></p>
Dataset for "Self-assembly of dodecagonal and octagonal quasicrystals in hard spheres on a plane"
<p>This dataset contains supplementary data for the publication:<br> <em>Self-assembly of dodecagonal and octagonal quasicrystals in hard spheres on a plane</em><br> E. Fayen, M. Impéror-Clerc, L. Filion, G. Foffi, and F. Smallenburg</p> <p> </p> <p><strong>Contents:</strong><br> The folder Data contains subfolders for each of the simulations performed for the construction of Fig. 3 of the main paper. Each folder name contains the size ratio q, the fraction of large particles x_L, and the packing fraction e in the file name. Note that the fraction of large particles x_L is related to the quantity x_S used in the paper via x_L = 1 - x_S.</p> <p>For simulations that were run for longer times, an additional folder with the same naming convention is included in the subfolder Long.</p> <p>Each simulation subfolder includes:</p> <p>- A coordinate file "last.sph" representing the final configuration of the simulation in plain text format. In this file, the first line specifies the number of particles, the second line the box size and non-additivity parameter Delta, and the remaining lines the coordinates of the particles. Each line containing coordinates consists of a letter indicating particle species (a or b), three spatial coordinates (with the z-coordinate always zero), and the particle radius. All lengths are given in units of the large-particle diameter.</p> <p>- An image of the final particle configuration "snapshot.png".</p> <p>- An image representing the associated scattering pattern, obtained by taking the Fourier transform of the particle coordinates and plotting the result as a function of the 2D wave vector on a logarithmic color scale.</p> <p> </p> <p>Additionally, the main folder contains a set of HTML files ("table_q*.html") that provide an overview of the snapshots and scattering patterns for each size ratio (specified in the file name). The HTML table for each size ratio uses the images from the "Data" and "Data/Long" subfolders as appropriate, and depends on the included "SAtable.css" and "SAtable.js" files. Within each table, clicking on one of the entries will enlarge the associated images.<br> <br> </p>
Gut Metagenome Assemblies for Veseli et al. 2023
<p>A collection of anvi'o contigs databases for 408 human fecal metagenome assemblies from the study by Veseli et al. titled "High metabolic independence is a determinant of microbial resilience in the face of gut stress". These are publicly-available gut metagenomes originally obtained from several studies of the gut microbiome. See `METAGENOMES_INFO.txt` file for references and sample SRA accessions.</p> <p>The metagenomes were assembled individually using IDBA-UD as part of the anvi'o metagenomics workflow in anvi'o v7.1-dev. As part of this workflow, they were annotated with KEGG KOfams using `anvi-run-kegg-kofams` and a KEGG snapshot from December 12, 2020 (modules database hash value `45b7cc2e4fdc`). See manuscript and its reproducible workflow for details.</p>
Long-term studies of secondary succession and community assembly in the prairie-forest ecotone of eastern Kansas, Hay meadow restoration experiment
Local and regional-scale processes interact to govern the assembly, diversity and functioning of ecological communities. Evaluating the interplay of these differently-scaled processes in the regulation of ecological systems is a challenging problem, but is crucial towards understanding and predicting the potential effects of accelerated human activity on biological diversity and ecosystem sustainability. Since 2000, two long-term field experiments have been underway in grasslands of eastern Kansas to investigate the interplay of soil resource availability, species interactions and regional processes governing plant secondary succession, community assembly, biodiversity, and ecosystem functioning. Both experiments involve manipulations of soil nutrients in permanent grassland study plots and employ multi-species seed addition treatments to evaluate the contribution of dispersal limitation and regional constraints on local species pools to the regulation of plant community dynamics. Hay meadow restoration experiment, previously funded by USDA, was established in 2000 in a section of the field that was left unplowed at the start of the experiment. Thus Experiment 2 was initiated in the context of secondary succession on recently abandoned cool-season hayfield where hay grass species were dominant at the start of the study. In this experiment we have been monitoring plant community change annually since 2001 in response to two aspects of hay management important in our area: annual fertilization and annual haying. The experimental design involves factorial manipulations of nutrient supply (two levels of NPK fertilization), annual haying (two levels: hayed; not hayed) and propagule input achieved by adding seeds of 41 native prairie species to half of the plots. Experiment 2 parallels Experiment 1 with manipulations of soil resources and species pools, but does so in the contexts of hay management and native prairie hay meadow restoration.
Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
<p>Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of <em>in vitro</em> grown plants) were sequenced and <em>de novo</em> assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> .</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly.tar.gz">CE_Assembly.tar.gz</a> - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly_fpkm.tar.gz">CE_Assembly_fpkm.tar.gz</a> - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/nt.db_CE_assembly.tar.gz">nt.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">swissprot.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (<a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">s</a>wissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/pfam30.db_CE_assembly.tar.gz">pfam30.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10<sup>-3</sup>.</p>
Rehti रहती (सिहोर जिला Madhya Pradesh). Temple remains re-assembled as plinth.
<p>Rehti रहती (सिहोर जिला Madhya Pradesh). Temple remains re-assembled as plinth, detail of temple balustrade.</p>
Eigen scores for human genome assembly GRCh38 Part 4 (Chr1 - Chr2)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
Eigen scores for human genome assembly GRCh38 Part 3 (Chr3 - Chr5)
<p>Eigen is a spectral approach to the functional annotation of genetic variants in coding and noncoding regions. Eigen makes use of a variety of functional annotations in both coding and noncoding regions (such as protein function scores, evolutionary conservation scores, and epigenetic annotations from ENCODE and Roadmap Epigenomics projects), and combines them into one single measure of functional importance. Eigen is an unsupervised approach, and, unlike many existing methods, is not based on any labelled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and subsequently uses these estimates of accuracy to derive the aggregate functional score for variants of interest as a weighted linear combination of individual annotations.</p>
Scored protein-protein interactions accompanying "A pan-plant protein complex map reveals deep conservation and novel assemblies"
<p><a href="http://plants.proteincomplexes.org/static/data/panplant_cfms_scores_annot.txt.gz">All scored pairwise protein-protein interactions with CF-MS scores (3,076,999 unique pairwise interactions)</a></p> <ul> <li>Description: Scores between Orthogroups with the corresponding CF-MS score and eggNOG generated orthogroup descriptions.</li> <li>Note: Only the highest scoring pairs are considered significant. A CF-MS score >= 0.509 corresponds to 10% FDR, >= 0.207 corresponds to 50% FDR</li> <li>Format: OrthogroupID1 [tab] OrthogroupID2 [tab] Score [tab] Annotation1 [tab] Annotation2</li> </ul>
Metagenomics of a pustular microbial mat from Shark Bay, Australia: Raw sequences and assembled MAGs
<p>This data accompanies the paper, "<a href="https://www.nature.com/articles/s43705-022-00128-1">Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats</a>" which looks at the cycling of sulfated polysaccharides in peritidal pustular mats from Shark Bay, Australia. The microbial community was sequenced, assembled, and binned. The raw sequencing reads used in this analysis are the following:</p> <ul> <li>SB_forward_paired_copy.fastq.gz </li> <li>SB_reverse_paired_copy.fastq.gz </li> </ul> <p>The resulting metagenome-assembled genomes (MAGs) are presented in the following folder:</p> <ul> <li>MAGs.zip</li> </ul> <p> </p> <ul> </ul> <p> </p>
Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus"
<p><em>Miscanthus sacchariflorus</em> (Maxim.) Hack. is a C4 perennial rhizomatous biofuel grass crop. <em>M. sacchariflorus</em> is among the most widely distributed species within the genus, particularly at cold northern latitudes, and one of the progenitor species of the main biomass commercial crop <em>M. × giganteus</em>. We generated a 2.54 Gbps whole-genome assembly of the diploid <em>M. sacchariflorus</em> “Robustus 297” genotype, which represented ~59% of the expected genome size. We later anchored this assembly in the chromosomal-scale <em>M. sinensis</em> genome to improve its contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored, respectively. We estimated our assemblies include ~85% of the <em>M. sacchariflorus</em> genes based on homology, core markers and RNA-seq alignments stats. Raw data and further metadata are available under Bioproject PRJNA435476.</p> <ul> <li>Msac_v2.fasta: Unanchored whole-genome assembly (WGA) of M. sacchariflorus in FASTA format.</li> <li>Msac_v3.fasta: The previous WGA re-scaffolded with the M. sinensis public reference.</li> <li>Msac_v3.agp: Chromosomal position in the M. sinensis reference of the previous scaffolds in Msac_v3.fasta</li> <li>Msac_v2.gff3: Gene annotation of the unanchored WGA in GFF3 format, which contains 86,767 coding genes</li> <li>Msac_v3.gff3: Gene annotation of the anchored WGA in GFF3 format, which contains 69,049 coding genes</li> <li>Msac_v2.func_annot.tsv: Text table containing the functional annotation of the 86,767 coding genes in Msac_v2.gff3</li> <li>Msac_v2.repeats_annotation.gff3: Repeats annotation (Repeatmasker) of the unanchored reference.</li> <li>Msac_v2.masked.fasta.gz: Repeats-masked version (Repeatmasker) of Msac_v2.fasta</li> <li>all.satsuma.blocks_Msac_v2-vs-Msin.gz: Every alignment from scaffolds in Msac_v3.fasta into M. sinensis reference</li> <li>Msac_v2.orthology_Msin.tsv: Ortologous between Msac_v2 and M. sinensis</li> <li>Msac_v3-vs-Msin.tsv: Ortologous between Msac_v3 and M. sinensis</li> </ul>
A2aR Oligomeric assemblies identified from MD simulations using in-vivo mimetic biomembranes
<p>GPCR oligomerisation is known to play an important role in the receptor signalling. However, due to the technical challenges, the structural information of GPCR oligomerisation is still very limited, which hinders our understanding of GPCR signalling in a fuller picture. In this deposit, we provide the structural coordinates of various oligomeric assemblies of Adenosine A2a receptor that were sampled from unbiased MD simulations.</p> <p>For more information regarding the MD simulation setup and definitions of the various calculated values, please check out our paper on <a href="https://www.biorxiv.org/content/10.1101/2020.06.24.168260v2">BioRxiv</a> (doi: https://doi.org/10.1101/2020.06.24.168260)</p> <p>** Simulation setup **<br> 9 copies of A2aR were randomly inserted into an <em>in-vivo </em>mimetic biomembrane (of size of 45nm x 45nm) to build the initial configuration of the simulations. 10 such systems were set up for A2aR in the inactive state, 10 for the active state and 10 for the active in complex with the mini Gs state. These systems were represented by MARTINI 2 coarse-grained models and were simulated for 50 micro-seconds. The use of MARTINI coarse-grained force field would freeze the receptor conformation in the initial configuration, thus decoupled the oligomerization from such process as ligand-induced conformational change. The more efficient sampling of coarse-grained force field therefore allowed us to explore fully the protein-protein associations in the oligomerisation process. Protein-protein associations were identified when any atoms from two protomers were getting closer than 0.75 nm. The oligomerisation process was monitored and the sampled various oligomeric assemblies were identified for calculation of oligomer residence time. </p> <p><br> ** Coordinate file explained **<br> These pdb files contain the A2aR oligomer structures in atomistic models. The coarse-grained oligomeric structures were converted back to atomistic models using CHARMM 36 force field. The identified oligomeric structures from each oligomeric order were clustered. 10 structures were randomly taken from each cluster and stored as individual models in the pdb files with a naming format <strong><em>{Conf. State}_OS{Oligomeric Order}_cl{Cluster id}.pdb</em></strong>. The pdb files can be viewed by such visualization tools as PyMol, Chimera or JMol etc.</p> <p><br> ** Spreadsheet file explained **<br> The calculated properties, including residence time and geometry, of each identified oligomer were stored in the Excel shreadsheet (Oligomeric_Assembly_Distribution.xlsx). Each oligomeric order, i.e. oligomer order = 2,3,4,5, opens an individual spreadsheet page where the calculated data were grouped by oligomers' conformational states (i.e. Inactive, Active and Act + mini Gs) and then ranked by oligomers' residence time. The measurements for describing the oligomer geometry were shown in columns after "Cluster ID" and before "Count". For definitions of these measurements, please refer to our paper. Pictures of the oligomers viewed from the extracellular side and intracellular side were also provided in the the spreadsheet to assist visualisation.</p>
Human assemblies evaluated in the hifiasm paper
<p>Human assemblies evaluated in the <a href="https://www.nature.com/articles/s41592-020-01056-5">Cheng et al (2021)</a>. Non-human assemblies are available at <a href="https://zenodo.org/record/4393750">doi:10.5281/zenodo.4393750</a>. File "*.ONT.*" were generated by <a href="https://www.nature.com/articles/s41587-020-0503-6">Shafin et al (2020)</a>, "*.DipAsm*" by <a href="https://www.nature.com/articles/s41587-020-0711-0">Garg et al (2020)</a> and "*.PAGS*" by <a href="https://www.nature.com/articles/s41587-020-0719-5">Porubsky et al (2020)</a>. The rest of the assemblies were generated by Cheng et al.</p>
Liftover of Drosoophila melanogaster genotypes, DGRP sample, from dm3 to dm6 reference assembly.
<p>Genotype data for Drosophila melanogaster DGRP collection.<strong> </strong>Variant positions relative to reference genome version dm6.<strong> </strong>Variant identifiers are in NCBI format.<strong> </strong>Processing code (including original data, reference sequences, perl scripts, etc).</p> <p>The initial intention of performing this 'liftover' was to allow comparison with data from a different melanogaster sample which had been analysed against a dm6 reference assembly. At the time of writing I am not aware that a dataset like this one exists.</p> <p>I've uploaded it in case it is useful to anyone in the future - and also as a trial of zenodo.</p> <p>See README.txt and flylifter.sh for more info.</p> <p> </p>
Research data supporting: "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"
<p>This repository contains the set of modelling data shown in the paper:<strong> "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"</strong>, published on Chemical Science (DOI: 10.1039/d3sc03930g)</p>
De novo transcriptome assembly of hyperaccumulating Noccaea praecox
<p>Trinity de novo assembly for hyperaccumulating plant species Noccaea praecox (syn. Thlaspi praecox), Brassicaceae. The dataset includes annotations from SwissProt, Pfam, Rfam databases and information on transmembrane regions and signal peptide cleavage sites (annotated using BLAST, HMMER, infernal, tmHMM and signalP through Trinotate). Detailed information on the preprocessing, assembly, post-processing and annotations are described in the ReadMe file.</p> <p>Supplementary material for Bočaj, V., Pongrac, P., Fischer, S. <em>et al.</em> <em>De novo</em> transcriptome assembly of hyperaccumulating <em>Noccaea praecox</em> for gene discovery. <em>Sci Data</em> <strong>10</strong>, 856 (2023). <a href="https://doi.org/10.1038/s41597-023-02776-x">https://doi.org/10.1038/s41597-023-02776-x</a></p>
Dataset for "Biocompatible Rhamnolipid Self-Assemblies with pH-Responsive Antimicrobial Activity"
<p>This dataset provides the raw data supporting the paper: Biocompatible Rhamnolipid Self-Assemblies with pH-Responsive Antimicrobial Activity. It comprises SAXS data (Figure 2, Figure 3, Figure 4, Figure 5, Figure S2 and Figure S4), cryo-TEM images (Figure 2D, Figure 4D, Figure 5D, Figure 5E), Zeta-potential measurment (Figure 7), DLS data (Figure 8, Figure S5, Figure S6, Figure S7, Figure S8 and Table S2), Antimicrobial activity data (Figure 9, Table 1, Figure S9, Figure S10, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16 and Table S3), Cytotoxicity data (Figure 10), Colloidal stability images (Figure S1 and Figure S3) and Biofilm inhibition and biofilm eradication assay (Figure S11).</p><p> </p>
III PhasAGE International Conference - Design of novel functional amyloid assemblies - Lecture
<p>The III PhasAGE International Conference "Multiscale understanding of protein aggregation and biomolecular condensates in aging and disease" brought together members of the PhasAGE consortium as well as outstanding international speakers from multidisciplinary fields dedicated to unraveling the intricacies of protein aggregation and biomolecular condensates in the context of aging and disease. For details on the conference program please see https://phasage.eu/iii-phasage-international-conference/. </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.