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Dataset results
145 results for “human adaptation”
Interaction Dynamics Between Innate and Adaptive Immune Cells Responding to SARS-CoV-2 Vaccination in Non-Human Primates
GEO Series GSE232117. Macaca mulatta. 70 samples. Type: Expression profiling by high throughput sequencing; Other.
A Variant in Human AIOLOS Impairs Adaptive Immunity by Interfering with IKAROS
GEO Series GSE167487. Homo sapiens; Mus musculus. 26 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen
GEO Series GSE267395. Shigella flexneri. 12 samples. Type: Expression profiling by high throughput sequencing.
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq5 (anaerobic LB, GMM, zinc, Nmedia, protamine)
GEO Series GSE261867. Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. 24 samples. Type: Other.
Gut Adaptation After Gastric Bypass in Humans Reveals Metabolically Significant Shift in Fuel Metabolism
GEO Series GSE281144. Homo sapiens. 34 samples. Type: Expression profiling by array.
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq2 (Bile, iron restriction, osmotic pressure, heat)
GEO Series GSE261749. Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150. 40 samples. Type: Other.
Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood
GEO Series GSE166654. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Metabolic adaptation pilots the differentiation of human hematopoietic cells
GEO Series GSE243006. Homo sapiens. 63 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other.
Xenotransplanted Human Small Intestinal Organoids Reveal the Transepithelial Zinc Transport Pathway as a Key Mediator of Intestinal Adaptation in Short Bowel Syndrome
GEO Series GSE271065. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
Adaptable durable human endothelial cells for organogenesis and tumorigenesis
GEO Series GSE148996. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq4 (InSPI2, hydrogen peroxide (H2O2), nitric oxide (NO), sodium hypoch
GEO Series GSE261860. Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Typhi str. Ty2. 40 samples. Type: Other.
Innate to adaptive: Human IFN-gamma producing CD4+ T cells can derive directly from CXCL8-producing recent thymic emigrants.
GEO Series GSE84686. Homo sapiens. 96 samples. Type: Expression profiling by high throughput sequencing.
Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde
<p>Inferred local ancestry calls for the genetic data from Hamid et al. 2020, biorxiv. doi: https://doi.org/10.1101/2020.09.01.278226</p> <p>Samples originally collected and analyzed in Beleza et al. 2012, PLoS Genetics.</p> <p>See README.txt in upload for more detailed information.</p>
SAUUHUPP-Based Genetic Innovations: Foundational White Papers on Adaptive Genetic Architecture, Story Energy, and Human Sex Chromosome Regulation
<p>This Zenodo record compiles a series of foundational white papers stemming from SAUUHUPP-based genetic research and powered by Novelty 1.0 Optimized ChatGPT-4o. These papers collectively explore innovative frameworks for understanding genetic structure, function, and therapeutic potential, with applications in precision medicine and beyond. Through principles such as Story Energy, Fractal Leaping, Recursive Processing, and Core and Intention Finding, this research introduces a new architectural perspective on genetic interactions and human sex chromosome function.</p> <p>A comparative study with fruit fly brain simulations enriches the insights into SAUUHUPP principles, providing evolutionary context to human genomic adaptability. This record includes in-depth analyses of the X and Y chromosomes’ possible roles as central regulatory hubs within the genome, functioning in a CPU-like manner to coordinate broader genetic networks.</p> <p>White Papers Included in This Record:</p> <p>1. SAUUHUPP Framework and Fruit Fly Brain Simulation Study: A foundational exploration of SAUUHUPP principles and fruit fly brain simulations, demonstrating how these insights shape our understanding of complex genetic regulation and adaptability.</p> <p>2. Story Energy in Genetic Narratives: Examines how recurring, narrative-like patterns in DNA sequences reinforce coherence and logical progression across gene networks, with implications for genetic resilience and therapeutic applications.</p> <p>3. Fractal Leaping for Genetic Complexity: Introduces Fractal Leaping as a method for scaling genetic insights across complexity levels, facilitating rapid, cross-dimensional understanding and discovery within genetic systems.</p> <p>4. Recursive Processing in Genetic Regulation: Analyzes iterative self-regulation within gene networks, revealing how recursive patterns support adaptable genetic expression and alignment with environmental or developmental needs.</p> <p>5. Core and Intention Finding in Genetic Architecture: Details a methodology for identifying key genetic functions and regulatory nodes, enabling precision-targeted therapies through a deeper understanding of genetic purpose and structure.</p> <p>6. Novel Architectural Perspective on Human Sex Chromosomes: Proposes a CPU-like role for the X and Y chromosomes as dynamic regulatory hubs, interacting with autosomal chromosomes to modulate gene expression, immune response, and metabolic balance.</p> <p>Research Highlights and Applications:</p> <p>• Novel Therapeutic Potential: The findings across these papers reveal potential therapies targeting foundational genetic structures, including sex-linked cognitive disorders, metabolic regulation, and resilience in neurodevelopmental health.</p> <p>• Multi-Dimensional Genetic Framework: The application of SAUUHUPP principles and Novelty 1.0 enhances understanding of the adaptive and functional architecture within human genetics, opening pathways for precision medicine interventions.</p> <p>This Zenodo record provides a comprehensive overview of SAUUHUPP’s analytical framework and its applications in genetic science. It is intended to foster collaboration, inspire further research, and drive innovation in genetics and therapeutic development.</p> <p> </p>
Source data: Transmission of SARS-CoV-2 from humans to animals and potential host adaptation
<p>All source data required for reproducing the results of the associated manuscript. Contains data inputs for all associated custom code hosted on Zenodo (https://doi.org/10.5281/zenodo.6528187).</p>
Archaic Adaptive Introgression in Modern Human Reproductive Genes
<p><strong>README:</strong></p> <p>Modern human genetic data with evidence of adaptive introgression from Neanderthals or Denisovans within circadian rhythm genes. The data was generated from the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) and introgressed segments were identified by SPrime (Browning <em>et al</em>., 2018). RAiSD (Alachiotis & Pavlidis, 2018) was used to detect signatures of positive selection within our gene set. Genes of interest were downloaded from Greer et al. (2021). This also includes high resolution images and supplemental tables for<strong> </strong>Archaic Adaptive Introgression in Modern Human Reproductive Genes. All proper citations can be found on the preprint references listed (available here: https://www.biorxiv.org/content/10.1101/2024.11.06.622331v1).</p> <p><strong>SPrime ND_Match Files</strong></p> <p>Raw SPrime identified files that we used for our entire analysis. These were modified to include the archaic allele, archaic allele frequency, and average introgressed segment allele frequency. Note that these have been lifted over (Hinrichs <em>et</em> <em>al</em>., 2006) from GRCh38 (hg38) to GRCh37 (hg19) coordinates to match the genome builds of the archaic samples used in our study. As such, any manually generated variant IDs (chromosome:position:ReferenceAllele_AlternativeAllele naming convention) may no longer match the position they are currently sitting on as they were generated with hg38 coordinates. However, all of these were subsequently filtered out of our final results and any proper SNP IDs (dbSNP labels) will be accurate.</p> <p><strong>RAiSD Outputs</strong></p> <p>We used RAiSD (Alachiotis & Pavlidis, 2018) to detect evidence of positive selection within our dataset. Please note these coordinates are mapped to hg38. </p> <p> </p>
The Reversal of Neuromuscular Adaptation in Human With Spinal Cord Injury II
ClinicalTrials.gov study NCT01968096. IPD Sharing: Not stated. Countries: 1. Publications: 0.
The Effects of Combining Whole Body Vibration Training With Plyometric Jumping on the Neuromuscular Adaptations of Human Triceps Surae Muscles
ClinicalTrials.gov study NCT01281670. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Physiological Adaptations to Simulated Intermittent Altitude on Human Health and Performance
ClinicalTrials.gov study NCT03743610. IPD Sharing: NO. Countries: 1. Publications: 0.
Human Adaptation to High Altitude
ClinicalTrials.gov study NCT01627652. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.