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ShareScore release 0.9.0
Dataset results
47 results for “sequence simulation”
['RNA sequencing of zebrafish embryos under simulated microgravity conditions']
['To reveal the potential mechanisms involved in the dysfunction of antiviral immune responses under simulated microgravity conditions, we investigated the transcriptional changes related to the status of innate immune responses by RNA-seq with poly I:C or mock PBS treatment under Normal gravity or simulated microgravity conditions. Our results indicate that the retinoic acid inducible gene (RIG)-I-like receptor (RLR) and Toll-like receptor (TLR) signal pathways, which are both involved in the type-I interferon induction, are significantly inhibited by simulated microgravity effects.']
Steinernema carpocapsae Breton small RNA sequencing insect in vitro simulation system, from "The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of
GEO Series GSE85256. Steinernema carpocapsae. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA sequencing of zebrafish embryos under simulated microgravity conditions
GEO Series GSE145967. Danio rerio. 12 samples. Type: Expression profiling by high throughput sequencing.
Simulated nucleotide sequences for testing alignment-free genome distance estimates
<p>This repository contains (12×500=)6,000 pairs of nucleotide sequences that have been simulated for testing alignment-free genome distance estimates, as described in <a href="https://riojournal.com/article/36178/">Criscuolo (2019)</a>. Given an evolutionary distance <em>d</em> varying from 0.05 to 0.60 (step = 0.05), the program <a href="http://tree.bio.ed.ac.uk/software/seqgen/">SeqGen</a> was used to simulate the evolution of 500 nucleotide sequence pairs with <em>d</em> substitution events per character (GTR+Γ evolutionary model).</p> <p>For each of the 12 evolutionary distances <em>d</em> = 0.05, 0.10, ..., 0.60, an XZ-compressed file containing 500 lines is available. Each line contains 18 fields separated by blank spaces:<br> [1] seed value used during simulation,<br> [2] true evolutionary distance <em>d</em> between the two simulated sequences,<br> [3] total number of simulated characters,<br> [4] number of non-indel characters with nucleotide mismatch,<br> [5] number of non-indel characters,<br> [6-9] A, C, G, T frequencies used during simulation,<br> [10-15] GTR parameters used during simulation,<br> [16] Γ distribution parameter used during simulation,<br> [17-18] two simulated sequences with indel events as gaps.</p> <p>Of note, each pair of aligned sequences without gaps can be regenerated using <a href="http://tree.bio.ed.ac.uk/software/seqgen/">SeqGen</a> v1.3.4 with parameters from fields [1,3,6-16] and the following two-leaf model tree:</p> <pre>(t1:d,t2:0.000);</pre> <p>where <em>d</em> is given in field [2].</p> <p>___</p> <p>Criscuolo A (2019) <em>A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies</em>. Research Ideas and Outcomes, 5:e36178. doi:<a href="https://doi.org/10.3897/rio.5.e36178">10.3897/rio.5.e36178</a></p>
Next-generation sequencing aims to comparative analysis of macrophages infected with EPEC under normal gravity and simulated microgravity
GEO Series GSE151411. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing of human brain organoids to evaluate sex-specific and opto-FGFR-mediated responses to Simplified 5 Ion GCR Simulation
GEO Series GSE309755. Homo sapiens. 66 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive and realistic simulation of tumour genomic sequencing data.
<p>Simulated tumour genomic sequencing data relating to the publication "Comprehensive and realistic simulation of tumour genomic sequencing data."</p>
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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.