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1,003 results for “darkness”
Effect of ultradian light-dark cycles on the transcriptome of mice carying a human Per3 polymorphism
GEO Series GSE55495. Mus musculus. 30 samples. Type: Expression profiling by array.
Light-dark changes in the transcriptome of Dinoroseobacter shibae in co-culture with the dinoflagellate Prorocentrum minimum
GEO Series GSE53846. Dinoroseobacter shibae DFL 12 = DSM 16493. 2 samples. Type: Expression profiling by array.
RNA-Seq of S.pistillata samples exposed to a 6-months darkness
GEO Series GSE171268. Stylophora pistillata. 6 samples. Type: Expression profiling by high throughput sequencing.
Genomic evidence reveals SPA-regulated developmental and metabolic pathways in dark-grown Arabidopsis seedlings
GEO Series GSE112662. Arabidopsis thaliana. 9 samples. Type: Expression profiling by high throughput sequencing.
Effects of MDMA and Venlafaxine treatment in Dark Agouti rats
GEO Series GSE47541. Rattus norvegicus. 46 samples. Type: Expression profiling by array.
Stimulation of cell elongation by tetraploidy in hypocotyls of dark-grown Arabidopsis seedlings
GEO Series GSE69349. Arabidopsis thaliana. 3 samples. Type: Expression profiling by array.
RNA Seq analysis of dark-grown hypocotyl comparing wild type with shr mutant.
GEO Series GSE106370. Arabidopsis thaliana. 4 samples. Type: Expression profiling by high throughput sequencing.
Halobacterium NRC-1 Diurnal experiment Dark 1
GEO Series GSE7709. Halobacterium salinarum NRC-1. 36 samples. Type: Expression profiling by array.
Brain gene expression data from High Drinking in the Dark (HDID) and HS/Npt control mice
GEO Series GSE93311. Mus musculus. 168 samples. Type: Expression profiling by array.
Fig. 2. Schizodon dissimilis, MCZ 19383, Lectotype 264.6 in Redescription of Schizodon dissimilis and appraisal of the dark barred species of the genus (Characiformes: Anostomidae)
Fig. 2. Schizodon dissimilis, MCZ 19383, Lectotype 264.6 mm SL, rio Poti, Piauí state.
Evidence for simultaneous occurrence of single dark band and periodic MSTIDs over geomagnetic low-mid latitude transition region
<p>Allsky Airglow Imager Data (630.0 nm) from Hanle, Leh Ladakh, India.</p> <p>Ionograms from New Delhi Digisonde.</p> <p> </p>
Data accompanying "Switching dynamics of dark-pulse Kerr comb states in optical microresonators"
<p>This dataset contains figure plotting scripts and corresponding raw measurement data for the paper "Switching dynamics of dark-pulse Kerr comb states in optical microresonators"</p>
Figure 8 from: Vahtera V, Stoev P, Akkari N (2020) Five million years in the darkness: A new troglomorphic species of Cryptops Leach, 1814 (Chilopoda, Scolopendromorpha) from Movile Cave, Romania. ZooKeys 1004: 1-26. https://doi.org/10.3897/zookeys.1004.58537
Figure 8 Likelihood tree with bootstrap values > 50% shown for each node.
Replication archive for Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification"
<p>This archive contains data and code for replicating all tables and figues in Burlig and Preonas, "Out of the Darkness and Into the Light? Development Effects of Rural Electrification". We include a README file as well as raw and intermediate data files. To replicate the paper's analysis, users can start with intermediate datasets at step A1 in MASTER.do. We also provide code and instructions to execute a full replication starting from raw data --- all of which is included in this archive and at these 4 Zenodo links:</p> <p>https://zenodo.org/records/10416551</p> <p>https://zenodo.org/records/10416621</p> <p>https://zenodo.org/records/10420499</p> <p>https://zenodo.org/records/10420771</p> <p> </p>
Figure 5 from: Karakasi D, Paragamian K, Mylonas M, Vardinoyannis K (2024) What`s crawling in the dark? An annotated list of gastropods in Greek caves. Subterranean Biology 48: 73-116. https://doi.org/10.3897/subtbiol.48.113383
Figure 5 Number of endemic and non-endemic cave-dwelling gastropods in Greek caves.
Figure 3 from: Karakasi D, Paragamian K, Mylonas M, Vardinoyannis K (2024) What`s crawling in the dark? An annotated list of gastropods in Greek caves. Subterranean Biology 48: 73-116. https://doi.org/10.3897/subtbiol.48.113383
Figure 3 Ecological classification of the cave-dwelling gastropods in Greek caves.
Figure 4 from: Karakasi D, Paragamian K, Mylonas M, Vardinoyannis K (2024) What`s crawling in the dark? An annotated list of gastropods in Greek caves. Subterranean Biology 48: 73-116. https://doi.org/10.3897/subtbiol.48.113383
Figure 4 Troglobiont gastropod species of Greece.
Data for "Microphysics of early dark energy"
<p>Data to reproduce figures in "Microphysics of early dark energy" (arXiv: 2202.08291). For questions please contact Vivian I. Sabla. </p>
Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems
<p><strong>Scripts for the paper "Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems"</strong></p> <p>DOI (BioRxiv): <a href="https://doi.org/10.1126/sciadv.add8911">10.1126/sciadv.add8911 </a></p> <p>In this project we have searched for genes associated with CRISPR-Cas systems from bacteria of the ESKAPE group using Random Forest and we have been able to reduce the percentage of CRISPR black matter, as well as to propose a triad 'Membrane Proteins - Phages - CRISPR' by which bacterial genomes would acquire CRISPR-Cas systems when they have certain useful membrane proteins that can act as viral receptors.</p> <p><strong>Python scripts</strong></p> <p>Package versions: matplotlib 3.5.0 numpy 1.19.2 pandas 1.3.5 scikit-learn 1.0.2 scipy 1.6.2 seaborn 0.11.2</p> <p><strong>Random forest inference</strong></p> <p>The script utilizes scikit-learns mean decrease in impurity feature importance measre to infer genes that set crispr containing strains apart from those without crispr systems. Cas-genes have been removed in the data, to allow to detect non Crispr-Cas related genes.</p> <p><strong>Jaccard distances</strong></p> <p>This script computes the Jaccard dissimilarity between the MLST groups which is used as distance measurement for a hierarchical clustering and dendrograms available in the papers supplementary data.</p> <p><strong>Correlation plot</strong></p> <p>This script uses the Jaccard indices of the jaccard-panel.py script, so the latter needs to be run beforehand. It plots the correlation plot featured in the paper.</p> <p><strong>Perl scripts</strong></p> <p><strong>addColumnFromABfile.pl</strong><br> Create an output to add to the metadata table, from a file with 2 columns: metadata ID.</p> <p><strong>addColumnsFromABfile.pl</strong><br> Creates an output with several columns to add to the metadata table, from a list of files, each with a list of IDs.</p> <p><strong>analyseSpacers.pl</strong><br> Calculate proportions of genomes with unique spacer/phages in two different clusters.</p> <p><strong>calculatePercentGenesInStrainsID.pl</strong><br> Calculate both absolute and relative frequency of pangenome genes in two clusters of genomes.</p> <p><strong>collectGFFMetadata.pl</strong><br> Collect all the information of the different strains and groups them in a final table</p> <p><strong>countGenesAndShareGenesFromPangenome.pl</strong><br> Count genes and average number of shared genes for each genome in the pangenome.</p> <p><strong>createComparisonMatrix.pl</strong><br> Create matrix for heatmaps comparing genes vs genomes.</p> <p><strong>createMatrixPresenceAbsence.pl</strong><br> Create gene presence/absence matrix.</p> <p><strong>delete_FP.pl</strong><br> Identify false positives by comparing spacers and direct repeats</p> <p><strong>extractSpacers.pl</strong><br> Extract spacers with evidence code 4 from CRISPRCasFinder results.</p> <p><strong>filterBlast_vs_db.pl</strong><br> Filter Blast hits with a given identity and subject coverage.</p> <p><strong>filter_spacers_vsall.pl</strong><br> Filter the results obtained from the comparison of spacers with different databases</p> <p><strong>find_cluster_cas.pl</strong><br> Find cas gene cluster from ccfinder results</p> <p><strong>getGroupsFromPangenome.pl</strong><br> Count appearances of each gene in the pangenome.</p> <p><strong>joinGFFwithCRISPR_v2.pl</strong><br> Prepare contigs from each genome as a string of gene names.</p> <p><strong>phage_vs_spacers.pl</strong><br> Compare a list of spacers against a phages database.</p> <p><strong>putSma3sGenenames2roaryClusters.pl</strong><br> Modify gene names assigned by Sma3s to avoid redundant names.</p> <p><strong>removeAssemblies.pl</strong><br> Check assembly files and remove those from GenBank when RefSeq is available.</p> <table> <tbody> <tr> <td><strong>Pangenomes files</strong></td> </tr> <tr> </tr> </tbody> </table> <p>If you want to download these files, please see "<em>url pangenomes files</em>"</p>
Dark Blade Idle Pose
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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.