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13,587 results for “specification”
Epigenome-wide analysis reveals specific DNA hypermethylation of T cells during human hematopoietic differentiation
<p>Epigenetic regulation plays an important role in cellular development and differentiation. A detailed map of the DNA methylation dynamics that occur during cell differentiation would contribute to decipher the molecular networks governing cell fate commitment. In this study we used the most recent Illumina MethylationEPIC Beadchip platform to describe the genome-wide DNA methylation changes observed throughout hematopoietic maturation by analyzing multiple hematopoietic cell types at different developmental stages.</p>
Marriage Proportion, Age Specific Fertility, Births within Marriage ratios for US, Japan, and selected European countries
<p>Dataset to accompany the paper "Marital fertility patterns and nonmarital birth ratios: an integrated approach"</p> <p>Includes:</p> <p>US African American women and White American women data on age-specific fertility (5-year groups), age specific marital fertility (5-year groups), proportion of women with a first marriage (5-year groups), and the ratio of births within marriage (5-year groups) as well as calculated values from the paper. For ages 15-44 and years 1980, 1985, 1990, 1995, 2000.</p> <p>Selected European country women data on age-specific fertility (5-year groups), age specific marital fertility (5-year groups), proportion of women with a first marriage (5-year groups), and the ratio of births within marriage (5-year groups) as well as calculated values from the paper. For ages 15-44 and years 1991, 2001, and 2011 (data not available for all countries in all years).</p> <p>Japanese women data on age-specific fertility (5-year groups), age specific marital fertility (5-year groups), proportion of women with a first marriage (5-year groups), and the ratio of births within marriage (5-year groups) as well as calculated values from the paper. For ages 15-44 and years 1950, 1960, 1970, 1980, 1990, 1995, 2000, 2005, and 2010.</p> <p> </p>
Spontaneous Low-Voltage Fast Onset Seizures in Human Mesial Temporal Lobe Epilepsy Are Caused by Specific Inhibitory/Excitatory Imbalance
<p>Local field potential recordings during low voltage fast seizures recorded from microelectrodes in patients with medically refractory temporal lobe epilepsy</p>
Platform Specific Metamodel in Ecore for developing learning ecosystems
<p>The learning ecosystem metamodel is a M2-model instantiated from Ecore, a M3-model in the four-layer metamodel architecture of OMG. The main objective of this metamodel is to provide a Platform Specific Model (PSM) for describing learning ecosystems build from Open Source software components, human elements and information flows between components which are represented by web services.</p>
Research data supporting "Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using 2 Compact Quantum Dot−DNA Conjugates"
<p>Raw research data supporting the publication:</p> <p>Wang, Y. et al., 2018, ACS Applied Materials & Interfaces, "Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using 2 Compact Quantum Dot−DNA Conjugates", DOI: 10.1021/acsami.8b07250.</p>
DBv5 features and codified complexes used in BIPSPI: a method for the prediction of partner-specific protein–protein interfaces
<p>Features and protein complexes codified for DBv5 BIPSPI paper</p> <p>(BIPSPI: a method for the prediction of partner-specific protein–protein interfaces</p> <p><a>Ruben Sanchez-Garcia</a> <a>C O S Sorzano</a> <a>J M Carazo</a> <a>Joan Segura</a></p> <p><em>Bioinformatics</em>, bty647, <a href="https://doi.org/10.1093/bioinformatics/bty647">https://doi.org/10.1093/bioinformatics/bty647</a>)</p>
Supplementary data to: Detection of Neoantigen-specific T Cells Following a Personalized Vaccine in a Patient with Glioblastoma
<p>Supplemental Data for the patient described in the manuscript: "Detection of Neoantigen-specific T Cells Following a Personalized Vaccine in a Patient with Glioblastoma". Summary of somatic variant calls from DNA whole exome, gene FPKM from RNA sequencing, and neoantigen predictions for high-affinity (ic<sub>50</sub> <500 nM) candidates.</p>
Data supporting the publication "Multi-use of the sea: a wide array of opportunities from site-specific cases across Europe"
<p>Data supporting the publication "Multi-use of the sea: a wide array of opportunities from site-specific cases across Europe"</p>
Cell specificity of human regulatory annotations and their genetic effects on gene expression
<p>Processed data for the manuscript: Cell specificty of regulatory annotations and their genetics effects on gene expression.</p> <p>The code to generate these data is included in the zip-file: regulatoryAnnotations_comparisons-master.zip</p> <p>and at GitHub: https://github.com/ParkerLab/regulatoryAnnotations_comparisons</p> <p>Individual dataset information:</p> <p>numberOfSegments.dat.gz: Number of segments in each annotation</p> <p>lengthDistributionOfSegments.dat.gz: Length distribution of segments in each annnotation</p> <p>genomeCoverage.dat.gz: Total genome coverage of regions in each annoation</p> <p>overlapFraction.dat.gz: Basepair level overlap between two pairs of annotations</p> <p>annotations_chromatinStateOverlap.dat.gz: Overlap of annotations with chromatin states</p> <p>information.fourcells_enhancer.dat.gz: Information content of the mean enhancer chromatin posterior probability for annotation segments across four cell types</p> <p>information.fourcells_promoter.dat.gz: Information content of the mean promoter chromatin posterior probability for annotation segments across four cell types</p> <p>gwas_enrichment_stats.txt.gz: Enrichment of GWAS SNPs in annotations</p> <p>GTEx_v7.ESI_medianTPM_min0.15.dat.gz : ESI for genes across 50 tissues</p> <p>gtexv7_lcleqtl.enrichment.dat.gz: Enrichment of GTEx v7 LCL eQTL in annotations</p> <p>gtexv7_lcleqtl.binned_lclESI.enrichment.dat.gz: Enrichment of GTEx v7 LCL eQTL binned by lclESI in annotations</p> <p>K562.gtexv7_bloodeqtl.fdr0.1.prune0.8.maf0.2.ld0.99.annotations.dat.gz: GTEx v7 blood eQTL effect sizes in K562 annotations </p> <p>GM12878.gtexv7_lcleqtl.fdr0.1.prune0.8.maf0.2.ld0.99.annotations.dat.gz: GTEx v7 LCL eQTL effect sizes in GM12878 annotations</p> <p>GM12878.dsqtl.prune0.8.maf0.2.ld0.99.annotations.dat.gz : GM12878 DNase QTL effect sizes in GM12878 annotations</p> <p>GM12878.allelicBiasResults.FracRef.downsampled30.annotations.withMAF.dat.gz: GM12878 ATAC-seq allelic bias effect sizes in GM12878 annotations </p> <p> <br> <br> <br> </p>
Anticipatory looking responses to specific satiety in adult humans.
<p>Data for an anticipatory looking experiment investigating adult humans' spontaneous responses to others' satiety.</p> <p>Further information, including compatible R analysis code, available on OSF.</p>
Main dataset 'Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity'
<p>Main dataset from the manuscript 'Environmental specificity in <em>Drosophila</em>-bacteria symbiosis affects host developmental plasticity' (2019)</p>
Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories
<p> </p> <p>Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.</p> <p> The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University.</p> <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv: Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> <p>This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal <em>Marine Micropaleontology.</em></p>
Integrated analysis of miRNA landscape and cellular networking pathways in stage-specific prostate cancer
<p><strong>Figure S1.</strong> Heat map of miRNA-microarray. Expression of miRNAs differentially expressed and assessed in microarray analysis of RNA isolated from four different cell lines of prostate cancer (LNCaP, PC3, DU145, 22Rv1) compared with control cell line of prostate cancer (PrEc). The red color depicts high and green color showed a lower level of expression at p value <0.01.</p> <p><strong>Figure S2A.</strong> Drug resistance by drug efflux. The internetworking relationship with miRNAs and plasma membrane protein P-glycoprotein (Pgp-plasma membrane protein). The miRNA-130a and miR-181a are downregulated in this pathway (green color) and linked with Pg and BCRP (breast cancer resistant protein). miR-133a and miR379 are involved in regulating the expression of MRP2. While miR-298, miR27a, miR331-5p and miR-130a are involved in regulating the expression of poly-glycoprotein (P-gp).</p> <p><strong>Figure S2B.</strong> Epithelial mesenchymal transition pathway. The miR-200b was downregulated during early-stage prostate cancer and was involved in inhibiting Jagged-2 (JAG2), one of the NOTCH ligands.</p> <p><strong>Figure S2C.</strong> Adipogenesis pathway. The expression of miR-326 was upregulated during the metastatic stage of prostate cancer, (red color) and involved in regulating the expression of CCAT/enhancer binding protein β (C/EBPβ), directly linked with the nuclear hormone receptor peroxisome proliferator-activated receptor-gamma (PPAR-γ).</p> <p><strong>Figure S2D.</strong> Bone metamorphosis signaling pathway. The expression of miR-140, miR-145, and miR-155 was upregulated, along with miR-140 and miR-145 were associated with modulation of gene SOX9, and miR-155 was involved in regulating the gene FOXO3A.</p> <p><strong>Figure S2E.</strong> Th1 pathway. In this pathway, the expression of miR-146a showed a higher level of expression (red color) and modulated the expression of NF-κB signaling.</p> <p><strong>Figure S2F.</strong> Th1 and Th2 pathway. In this pathway, the expression of miR-146a showed a lower level of expression (green color) and may modulate the expression of NF-κB signaling.</p> <p><strong>Table S1.</strong> List of differentially expressed miRNAs derived from LNCaP cells lines statistically significant as P < 0.001.</p> <p><strong>Table S2.</strong> List of differentially expressed miRNAs derived from PC3 cells lines statistically significant as P < 0.001.</p> <p><strong>Table S3.</strong> List of differentially expressed miRNAs derived from DU145 cells lines statistically significant as P < 0.001.</p> <p><strong>Table S4.</strong> List of differentially expressed miRNAs derived from 22Rv1 cells lines statistically significant as P < 0.001.</p>
MANOVA dataset 'Environmental specificity in Drosophila-bacteria symbiosis affects host developmental plasticity'
<p>MANOVA dataset from the manuscript 'Environmental specificity in <em>Drosophila</em>-bacteria symbiosis affects host developmental plasticity' (2019)</p>
Automatic and feature-specific prediction related neural activity in the human auditory system
<p>Downsampled (to 100Hz) data of the paper "Automatic and feature specific prediction related neural activity in the human auditory system"</p>
Gender Specific Cannibalism in male Phytoseiulus persimilis.
<p>This dataset was used to research if cannibalism by male <em>Phytoseiulus</em> <em>persimilis</em> was reared towards a specific gender. This was done by comparing the sex ratios in groups of individuals that experienced cannibalism in the larval stage to those who did not. </p>
Human-specific tandem repeat expansion and differential gene expression during primate evolution
<p>THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> <a href="https://www.pnas.org/content/early/2019/10/22/1912175116">https://www.pnas.org/content/early/2019/10/22/1912175116</a></p> <p> </p> <p>THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056</a></p> <p><br> ORIGINAL UPLOAD: 09/06/2019</p> <p>UPDATES: 10/28/2019; 01/27/2020</p> <p>DESCRIPTION: Contigs were assembled using Phased-SV (<a href="https://www.nature.com/articles/s41467-018-08148-z">Chaisson et al, Nature Communications 2019</a>) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in <a href="https://science.sciencemag.org/content/360/6393/eaar6343">Kronenberg et al, Science 2018</a>. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.</p>
Fig. 1 in Species-specific qPCR assays allow for high-resolution population assessment of four species avian schistosome that cause swimmer's itch in recreational lakes
Fig. 1. Abundance of cercariae by sampling site. Water samples were obtained in mid-June and cercariae abundance was determined using the pan-avian schistosomes qPCR.
Fig. 2 in Species-specific qPCR assays allow for high-resolution population assessment of four species avian schistosome that cause swimmer's itch in recreational lakes
Fig. 2. Percent contribution of T. stagnicolae, T. szidati, T. physellae and A. brantae species to each lake. Water samples from different locations and dates were tested using the species-specific qPCR assay and results were pooled by lake to understand the relative contribution overall of each species to each lake. The percent contribution (based on gene copy number) of each species was calculated.
Fig. 3 in Species-specific qPCR assays allow for high-resolution population assessment of four species avian schistosome that cause swimmer's itch in recreational lakes
Fig. 3. Lifecycles of T. stagnicolae, A. brantae, T. szidati, and T. physellae. life cycle summary of the avian schistosome species targeted for species-specific qPCR tests designed in this study.
ScienceDex guides
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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.