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88 results for “gene atlas”
Gene expression ATLAS of Arabidopsis thaliana (accession Columbia) across its lifecycle
<p><strong>Abstract: </strong>Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 gene expression libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.</p> <div><strong><span>Organism part: </span></strong><span>inflorescence, whole plant, seed, root, silique fruit, flower, rosette</span></div> <div> </div> <div><span><strong>Developmental stage:</strong> </span><span>LP.02 two leaves visible stage, IL.00 inflorescence just visible stage, fruit size 30 to 50% stage, LP.12 twelve leaves visible stage, root development stage, fruit size 70% to final stage, LP.06 six leaves visible stage, dry seed stage, flowering stage, seed imbibition stage, sporophyte senescent stage, inflorescence development stage</span></div> <div> </div> <div> <div><strong><span>Organism: </span></strong><span>Arabidopsis thaliana</span></div> <div> </div> <div><span><strong>Ecotype:</strong> </span><span>Col-0</span></div> <div> </div> <div><strong><span>Genotype: </span></strong><span>wild type genotype</span></div> <div> </div> <div><span><strong>Age:</strong> Samples are from </span><span>20-day, 49-day, 39-day, 15-day, 21-day, 9-day, 22-day, 55-day, 26-day, 45-day</span></div> <div> </div> <div><span><strong><span>Experimental Designs: </span></strong><span>growth chamber study<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://purl.obolibrary.org/obo/EO_0007269" target="_blank" rel="noopener"> EFO</a></span>, <span>development or differentiation design<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0001746" target="_blank" rel="noopener"> EFO</a></span>, <span>organism part comparison design<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0001750" target="_blank" rel="noopener"> EFO</a></span></span></div> <div> </div> <div><span>For more description of the data and sample types see the file <a href="../api/records/11133989/draft/files/PRJEB24664_Sample_descriptors.xlsx/content" target="_blank" rel="noopener noreferrer">PRJEB24664_Sample_descriptors.xlsx or visit </a> or visit <a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422/sdrf">https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422/sdrf</a></span></div> <div> </div> <div><span>Original data was submitted from </span></div> <div> <ul> <li><span>EMBL-EBI ArraExpress: <a href="https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422">https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422</a></span></li> <li><span>NCBI SRA: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJEB24664">https://www.ncbi.nlm.nih.gov/bioproject/PRJEB24664</a></span></li> </ul> <p><strong><span>Protocol description:</span></strong></p> <table> <tbody><tr> <th>Name</th> <th>Type</th> <th>Description</th> <th>Hardware</th> </tr> </tbody><tbody> <tr> <td>P-MTAB-71349</td> <td><span>growth protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0003789" target="_blank" rel="noopener"> EFO</a></span></td> <td>Seeds were planted in pots containing commercial potting mix with fertilizers. Pots were covered with clear perforated plastic wrap and kept at 4 degrees celsius for 3 days to break the dormancy. After 3 days plants were transferred to the Intellus Ultra growth chamber (Percival Scientific, IA, USA) which was set to temperature 22-23 degrees celsius, light intensity 120-150 micromol/m2sec under the cycle of 16h light and 8h dark. Soil was kept moist by gently spraying with water every 72 hours to maintain humidity to 50-60%. Sampling time point is given in days after germination.</td> <td> </td> </tr> <tr> <td>P-MTAB-71350</td> <td><span>nucleic acid extraction protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0002944" target="_blank" rel="noopener"> EFO</a></span></td> <td>Total RNA from frozen samples was extracted as a method described in Filichkin et al., 2010. Total RNA was used to isolate large RNA as per manufacturer's protocol for miRNeasy Mini kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA).</td> <td> </td> </tr> <tr> <td>P-MTAB-71351</td> <td><span>nucleic acid library construction protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0004184" target="_blank" rel="noopener"> EFO</a></span></td> <td>True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.</td> <td> </td> </tr> <tr> <td>P-MTAB-71352</td> <td><span>nucleic acid sequencing protocol<a title="" href="https://www.ebi.ac.uk/ols4/ontologies/efo/terms?iri=http://www.ebi.ac.uk/efo/EFO_0004170" target="_blank" rel="noopener"> EFO</a></span></td> <td>101bp paired-end sequencing of mRNA was performed by using the standard protocols on Illumina HiSeq 3000.</td> <td>Illumina HiSeq 3000</td> </tr> </tbody> </table> </div> </div>
Online Supplemental Tables - An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index
<p>Summary statistics of metabolite-gene expression associations and mediation analyses of effects on body mass index.</p> <p>The corresponding publication is currently under revision.</p> <ul> <li><strong>Online Supplemental Table 1</strong>: Gene expression-metabolite association summary statistics from 97 metabolites and metabolite ratios and up to 15175 genes calculated seperately in the LIFE-Adult, LIFE-Heart, LIFE-AMI and the Sorb studies. Associations were adjusted for six covariates.</li> <li><strong>Online Supplemental Table 2</strong>: Random-effects meta-analyzed gene expression-metabolite association summary statistics. P-Values were adjusted for multiple testing using a hierarchical adjustment procedure both on local (within phenotypes) and on global (across phenotypes) level.</li> <li><strong>Online Supplemental Table 3</strong>: Single-study association results needed for checking mediation analysis assumptions and for calculating mediation statistics. Only gene expression probe-metabolite pairs that associated significantly at hierarchical FDR=5% in the gene-expression-metabolite association meta-analysis qualified for these associations.The following Associations were tested: gene expression probes ~ metabolites, log-BMI ~ metabolites log-BMI ~ gene expression, log-BMI ~ gene expression + metabolite. Associations were adjusted for six covariates. P-values</li> <li><strong>Online Supplemental Table 4</strong>: Meta-analyzed association results needed for checking mediation analysis assumptions and for calculation mediation statistics.</li> <li><strong>Online Supplemental Table 5: </strong>Mediation analysis summary statistics. Mediations of gene expression effects (exposure) via metabolite effects (mediatior) and of metabolite effects (exposure) via gene expression effects (mediator) on body mass index (outcome) were tested.</li> </ul> <p> </p>
Cacao gene atlas: Additional file 13 (CPM normalized read counts) and Additional file 14 (fractional counts)
<p class="MsoNormal">A large dataset of replicated transcriptomes was developed to accelerate<span class="MsoCommentReference"> <em>T</em></span><em>heobroma cocoa</em> genomics research with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao. RNAs were extracted and transcriptomes were sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3-5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. We describe the creation of the atlas,and its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. To promote wider use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. A gene expression browser with a graphical user interface was developed to display gene expression patterns and to provide easy access of raw data and statistical analyses.</p>
The cacao gene atlas: A transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L
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Annotated genes harboring major effect markers (R2 ≥ 15%). Highlighted in green are genes annotated from Rhodes et al. 2014,2017, in orange genes annotated as similar to Peroxidase, in yellow new annotations from sorghum genome in Atlas. In the first three columns start and stop position on the sorghum genome and transcript name, followed by the nearest marker name and the distance of the gene from the nearest marker, then a column where are shown the GWAS methods and target traits for which the linked SNP was significant, the last column shows the category of the genes.
<p><strong>We conducted a comprehensive genomics study to map genomic loci determining the production of antioxidants in sorghum grains. Encouraging results were obtained and published in peer-reviewed article with impact factor (https://doi.org/10.1371/journal.pone.0225979). Annotated genes harboring major effect markers (R<sup>2</sup> ≥ 15%) were identified and will be of worldwide interest. </strong></p>
R data set: The Cancer Genome Atlas Gene Expression data
<p>This compound data set comprises the following information from the The Cancer Genome Atlas:</p> <ul> <li>RNA-Seq counts for 60483 genes across 11093 samples</li> <li>HuEx 1.0 ST gene expression data for 18632 genes across 1211 samples</li> <li>clinical indicators for 11160 patients</li> </ul> <p>All gene expression data is annotated across ENSEMBL, ENTREZ and symbols. Samples are annotated by TCGA barcodes.</p> <p>To read the data set into R (requires 6 GB of RAM) use:</p> <p>tcga <- readRDS("tcga.rds")</p>
datset of "Networks and genes modulated by posterior hypothalamic stimulation in patients with aggressive behaviours: Analysis of probabilistic mapping, normative connectomics, and atlas-derived transcriptomics of the largest international multi-centre dataset"
<p>This dataset accompanies the manuscript:<br> "Networks and genes modulated by posterior hypothalamic stimulation in patients with aggressive behaviours: Analysis of probabilistic mapping, normative connectomics, and atlas-derived transcriptomics of the largest international multi-centre dataset."<br> DOI: (https://doi.org/10.1101/2022.10.29.22281666)</p> <p>by</p> <p>Flavia Venetucci Gouveia1,2,3*†,Jürgen Germann4,5†, Gavin JB Elias4,5, Alexandre Boutet4,6, Aaron Loh4,5, Adriana Lucia Lopez Rios7,8, Cristina V Torres Diaz9, William Omar Contreras Lopez10,11, Raquel CR Martinez3,12, Erich T Fonoff13, Juan C Benedetti-Isaac14, Peter Giacobbe 2,15,16, Pablo M Arango Pava17, Han Yan5,18, George M Ibrahim5, 18,19,20, Nir Lipsman2,5,15, Andres M Lozano4,5, Clement Hamani2,5,15*</p> <p>1. Neuroscience and Mental Health, Hospital for Sick Children Research Institute; Toronto, Canada <br> 2. Sunnybrook Research Institute; Toronto, Canada<br> 3. Division of Neuroscience, Sírio-Libanês Hospital; São Paulo, Brazil<br> 4. Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, Canada<br> 5. Division of Neurosurgery, Department of Surgery, University of Toronto; Toronto, Canada<br> 6. Joint Department of Medical Imaging, University of Toronto; Toronto, Canada<br> 7. Department of Functional and Stereotactic Neurosurgery, University Hospital San Vicente Fundación,<br> Medellín, Colombia<br> 8. Department of Functional and Stereotactic Neurosurgery, San Vicente Fundación, Rionegro, Colombia<br> 9. Department of Neurosurgery, University Hospital La Princesa; Madrid, Spain<br> 10. Nemod Research Group, Universidad Autónoma de Bucaramanga; Bucaramanga, Colombia<br> 11. Division of Functional Neurosurgery, Department of Neurosurgery, FOSCAL Clinic; Bucaramanga,<br> Colombia<br> 12. LIM 23, Institute of Psychiatry, School of Medicine, University of São Paulo; São Paulo, Brazil<br> 13. Department of Neurology, Integrated Clinic of Neuroscience, School of Medicine, University of São Paulo;<br> São Paulo, Brazil.<br> 14. Stereotactic and Functional Neurosurgery Division of the International Misericordia Clinic; Barranquilla,<br> Colombia<br> 15. Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre; Toronto, Canada<br> 16. Department of Psychiatry, University of Toronto; Toronto, Canada<br> 17. Servicio de Neuocirugia Funcional y Esterotaxia, Clinica Comuneros Bucaramanga, Clinica Desa y Clinica<br> Dime Neurocardiovascular de Cali; Clinica Nueva del Lago, Bogota, Colombia.<br> 18. Division of Neurosurgery, The Hospital for Sick Children; Toronto, Canada<br> 19. Institute of Biomedical Engineering, University of Toronto; Toronto, Canada<br> 20. Institute of Medical Science, University of Toronto; Toronto, Canada<br> † Flavia Venetucci Gouveia and Jürgen Germann contributed equally to this work and share first authorship.</p> <p>* Corresponding Author: Dr. Flavia Venetucci Gouveia. Neuroscience and Mental Health, Hospital for Sick Children Research Institute. 686, Bay Street, Toronto, ON, M5G 0A4, Canada. flavia.venetuccigouveia@sickkids.ca<br> * Corresponding Author: Dr. Clement Hamani. Sunnybrook Research Institute. 2075 Bayview Ave, S126. Toronto, ON, M4N3M5, Canada. clement.hamani@sunnybrook.ca</p> <p>It contains a zip folder ("estimated_binary_Volume_of_Tissue_Activated.zip") with one file (in nii.gz format) per patient estimating the Volume of Activated Tissue for that patient (the estimated 'reach' of the active DBS stimulation) and a demographics file.<br> The case numbers are identical to Table 1 in the manuscript.</p>
Atlas of nascent RNA transcripts reveals enhancer to gene linkages
<p>Data associated with the paper "Atlas of nascent RNA transcripts reveals enhancer to gene linkages"</p> <p>GitHub repository for the analyses: <a href="https://github.com/Dowell-Lab/DBNascent_Analysis">https://github.com/Dowell-Lab/DBNascent_Analysis</a></p> <p>Below are the summaries of the files associated with this publication. </p> <p> </p> <p>1. muMerge calls for each paper used in the merging</p> <p><strong>paper_mumerge_calls</strong></p> <p>- The calls are separated by the bidirectional caller (dreg, tfit)</p> <p>- In the folders are bed files (e.g. <em>Allen2014global_hg38_dreg_MUMERGE.bed</em>) for each paper and species (hg38, mm10)</p> <p> </p> <p>2. Base content for regions called by dREG and Tfit in each paper in mouse and human</p> <p><strong>mumerge_base_composition</strong></p> <p>- The base content for each paper after the first round of muMerge</p> <p>- The files contain the id and the base nucleotide content in 300bp around the center region (id, cg, at)</p> <p> </p> <p>3. Bidirectional regions called by Tfit and dREG after merging. Regions are for mouse and human datasets. (See <a href="https://github.com/Dowell-Lab/bidirectionals_merged">https://github.com/Dowell-Lab/bidirectionals_merged</a>)</p> <p><strong>bidirectional_regions</strong></p> <p>- Bidirectional regions called after muMerge and filtering</p> <p>- Calls for both human and mouse datasets are reported (<em>hg38_tfit_dreg_bidirectionals.bed.gz</em> and <em>mm10_tfit_dreg_bidirectionals.bed.gz</em>)</p> <p>- The bed files are in bed6 format with the following columns:</p> <p>chromosome, start, stop, bidirectional, number of papers a bidirectional was called, strand (it is . since bidirectionals are not stranded)</p> <p> </p> <p>4. Metadata for samples used in the SPECS and correlation analysis</p> <p><strong>metadata</strong></p> <p><span> - Sample metadata for filtered samples (human_samples_QC_GC_protocol_filtered.tsv.gz) in the downstream analyses </span></p> <p> </p> <p>5. SPECS scores across genes and bidirectional regions</p> <p><strong>specs_scores</strong></p> <p><span> - The SPECS scores for all tissues analyzed (filt_qc123_all_specs_all.txt.gz) are reported,</span></p> <p><span> - Along with the maximum (filt_qc123_all_specs_maxval.txt.gz) </span></p> <p><span> - And minimum SPECS scores (filt_qc123_all_specs_minval.txt.gz).</span></p> <p><span> - The SPECS scores were also split by disease vs non-disease samples</span></p> <p><span> - The TPMs summaries are also included</span></p> <p> </p> <p><span>6. Normalized counts </span></p> <p><strong><span>normalized_counts</span></strong></p> <p><span> - Gene and bidirectional region normalized counts (gene_bidir_tpm.tsv.gz)</span></p> <p> </p> <p>7. Bidirectional Region and gene pairs (See https://github.com/Dowell-Lab/bidir_gene_pairs)</p> <p><strong>bidirectional_gene_pairs</strong></p> <p>- Gene and bidirectional region pairs (<em>dbnascent_pairs.txt.gz</em>) across tissues in high-quality samples. </p> <p>- The pairs are reported in a bed12 file</p> <p> - Where the first 6 columns are gene coordinates and the following 6 are bidirectional coordinates.</p> <p> - The remaining columns are the summary statistics for correlation and the relationship between the gene and bidirectional.</p> <p><span> - Additional columns note whether the pair overlaps eQTLs from GTEx (eQTL) or polII ChIA-PET loops</span></p> <ul> <li>transcript1_chrom : Gene chromosome</li> <li>transcript1_start : Gene start coordinate</li> <li>transcript1_stop : Gene stop coordinate</li> <li>transcript_1 : Gene id</li> <li>transcript1_score : Gene score (. since none was assigned)</li> <li>transcript1_strand : Gene strand</li> <li>transcript2_chrom : Bidirectional chromosome</li> <li>transcript2_start : Bidirectional start coordinate</li> <li>transcript2_stop : Bidirectional stol coordinate</li> <li>transcript_2 : Bidirectional id</li> <li>transcript2_score : Bidirectional score (i.e. the number of papers that support a bidirectional from muMerge)</li> <li>transcript2_strand : Bidirectional strand (. since these are not stranded)</li> <li>pcc : Pearsons correlation coefficient</li> <li>pval : P-value</li> <li>adj_p_BH : Adjusted p-value (Benjamini-Hochberg correction)</li> <li>nObs : Number of observations in correlation analysis</li> <li>t : T statistic</li> <li>distance_tss : Distance between the gene start (TSS) and the bidirectional start coordinate</li> <li>distance_tes : Distance between the gene stop (TES) and the bidirectional start coordinate</li> <li>position : Is the bidirectional upstream or downstream of the TSS</li> <li>tissue : Tissue id based on metadata for tissue-derived correlations (labeled All_samples if all samples are used)</li> <li>percent_transcribed_both : Percent of the number of observed samples used in the analysis</li> <li><span>pair_id : Gene:Transcript~Bidirectional pair name</span></li> <li><span>gene_id : Gene id</span></li> <li><span>chiapet : Binary indicator for whether pair overlaps overlap polII ChIA-PET </span></li> <li><span>gtex : Bindary Indicator whether a pair is overlapping GTEx pairs</span></li> </ul> <p> </p>
Association between Galectin-1 gene expression and acute myeloid leukemia patient survival in The Cancer Genome Atlas
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Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes
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Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species
C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.
Comprehensive Atlas of Almond R genes reveals new insight on NBS domain evolution
<p>GFF files of the manually curated R genes in almond and the fasta file for proteins. The best model for each genes were found in either F0 and F1 files corresponding to the phased haplotypes published in <a href="https://doi.org/10.1093/hr/uhae106">https://doi.org/10.1093/hr/uhae106</a></p>
Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species
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An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [bulk RNA-seq]
GEO Series GSE182672. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
An atlas of gene regulatory networks for T memory cells in youth and old age [scATAC-seq]
GEO Series GSE228660. Mus musculus. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A single-cell atlas of human brain middle temporal gyrus reveals sex-specific and cell-type-specific gene expression regulation in Alzheimer’s disease
GEO Series GSE188545. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Atlas of nascent RNA transcripts reveals high confidence enhancer associated bidirectionals linked with genes across different tissue types
GEO Series GSE227931. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Single-cell profiles of retinal neurons differing in resilience to injury reveal neuroprotective genes - Atlas of adult mouse retinal ganglion cells
GEO Series GSE133382. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
An Arabidopsis root phloem pole cell atlas reveals PINEAPPLE genes as transitioners to autotrophy [10x scRNA-seq]
GEO Series GSE181999. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Atlas of target genes of thyroid hormone (TH) in mice
GEO Series GSE210975. Mus musculus. 3 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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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.