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3,696 results for “reference”
Attosecond Short References
<p>References and supplemental materials for the attosecond short.</p>
Electromagnetic Spectrum Short References and Supplement Materials
<p>References and Supplement Materials for the Electromagnetic Spectrum Short</p>
LINGUISTIC-CULTURAL STUDY OF THE MEANS REPRESENTING THE CATEGORY OF REFERENCE
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NSG-adapted reference genome - TRACERx PDX study
<p>NSG-adapted mouse reference genome and scripts to reproduce the results from whole-genome sequencing data derived from the tail of a male NOD SCID gamma (NSG) mouse (Mus musculus). The mouse was purchased from Charles River and had carried a subcutaneous human non-small cell lung cancer xenograft.</p> <p>The raw whole-genome sequencing data are available on ENA under accession number PRJEB65917 (https://www.ebi.ac.uk/ena/browser/view/PRJEB65917).</p> <p>The original manuscript describing this sample is available here.</p>
Fig. 30 in Diversity and taxonomy of the Late Triassic sauropodomorphs (Saurischia, Sauropodomorpha) stored in the Palaeontological Collection of Tübingen, Germany, historically referred to Plateosaurus
Fig. 30. Skeletal elements of specimen GPIT-PV-30789 on display in the diorama, referred to as Plateosaurus 'quenstedti' by von Huene (see Fig. 14) comprising a right hindlimb, with a femur, a tibia, a fibula, and a complete pes.
IMPACT OF DIGITIZATION ON STUDENTS PERFORMANCE: A STUDY WITH REFERENCE TO SELECTED HIGHER SECONDARY SCHOOLS IN BHOPAL CITY
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Dataset related to article "Standardized Diagnostic Reference Levels for Paediatric Interventional Cardiology: data from an Italian referral centre"
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Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files</p>
Reference Energy System for Off-Grid Sectors
<p>This diagram illustrates a reference energy system designed for various off-grid sectors (residential, commercial, agriculture, etc.).</p> <p>This visual aid can support the development of models on OSeMOSYS, LEAP, TIMES, or other energy modelling tools, as well as facilitate the integration of energy planning models like OnSSET and OSeMOSYS, or others.</p> <p>This material has been produced with support from the Climate Compatible Growth (CCG) programme. CCG is funded by UK aid from the UK government. However, the views expressed herein do not necessarily reflect the UK government's official policies. </p>
The influence of the socio-economic characteristics in the corporate social responsibility initiatives: a reference to cause-related marketing
<p>Ponencia - IV Congreso Latinoamericano de Marketing Social</p>
High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae
<p>Output files from the assembly of 2 reference genomes detailed in the publication Rivera et al. 2024. High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks <em>Spondylurus nitidus</em> and <em>S. culebrae. Genome Biology and Evolution</em>, evae079.</p>
two-day International Online Workshop on Reference Management and Zotero Software conducted on 29-30 May 2021.
<p>two-day International Online Workshop<br>on Reference Management and Zotero Software conducted on 29-30<br>May 2021.</p>
Three reference genomes for freshwater diatom ecology and evolution
<p>This repository contains the genome assemblies and gene models provided for "Three reference genomes for freshwater diatom ecology and evolution"</p> <p>Authors:</p> <p>Wade R. Roberts (email: wader [at] uark [dot] edu)</p> <p>Andrew J. Alverson (email: aja [at] uark [dot] edu)</p> <p> </p> <p>The Whole Genome Shotgun (WGS) projects are available from NCBI GenBank under accession JALLPB020000000 (C. tholiformis), JALLBG020000000 (D. pseudostelligera), and JALLAZ020000000 (P. triporus).<strong></strong></p> <p><br>The following files are included:</p> <p>Cyclostephanos tholiformis strain AJA228-03</p> <p> aja228-03.consensus.fasta</p> <p> aja228-03.consensus.gff3<br> <br> aja228-03.consensus.proteins.fasta</p> <p> aja228-03.consensus.combined_uniprot_annotation.csv</p> <p> aja228-03.consensus.panther_annotation.csv</p> <p> aja228-03.consensus.pfam_annotation.csv</p> <p> </p> <p>Discostella pseudostelligera strain AJA232-27</p> <p> aja232-27.consensus.fasta</p> <p> aja232-27.consensus.gff3<br> <br> aja232-27.consensus.proteins.fasta</p> <p> aja232-27.consensus.combined_uniprot_annotation.csv</p> <p> aja232-27.consensus.panther_annotation.csv</p> <p> aja232-27.consensus.pfam_annotation.csv</p> <p> </p> <p>Praestephanos triporus strain AJA276-08</p> <p> aja276-08.consensus.fasta</p> <p> aja276-08.consensus.gff3<br> <br> aja276-08.consensus.proteins.fasta</p> <p> aja276-08.consensus.combined_uniprot_annotation.csv</p> <p> aja276-08.consensus.panther_annotation.csv</p> <p> aja276-08.consensus.pfam_annotation.csv</p> <p> </p> <p>R code and phylogenetic tree to reproduce Figure 1 in the manuscript</p> <p> plot-figure-1.R</p> <p> busc.prot.concat.partition.rooted.tree</p> <p> </p>
Fig. 1 in A New Genus and Two New Species of the Family Aulopidae (Aulopiformes), Commonly Referred to as Aulopus, Flagfins, Sergeant Bakers or Threadsails, in Australasian Waters
Fig. 1. TN93 neighbour-joining tree of 59 COI sequences from 4 purported genera and 11 purported species of Aulopidae, as well as sequences for an outgroup species, Paraulopus nigripinnis. Percent bootstrap values are given for all well supported nodes (>70%), followed by bootstrap values for these nodes in a TN93 maximum likelihood and a p-distance neighbour joining tree. See text. Specimen numbers are registration numbers of vouchers or those of the Barcode of Life Database (BOLD, www.barcodinglife.org) or GenBank (www.ncbi.nlm.nih. gov).
Fig. 2 in Microcrustacean (Cladocera, Copepoda) Communities In Artificial Lakes In The Region Of The North Hungarian Mountains, With Special Reference To The Adventive Species
Fig. 2. SDR-simplex of the microcrustacean communities of the 20 fish ponds. S, D and R refer to relativized similarity (S), richness difference (D) and species replacement (R)
Genomic reference data for calculating conditional & conjuncational false discovery rates with cfdr.pleio
<p><strong>Background</strong></p> <p>This data set provides genomic reference information extracted from the 1000 Genomes Project for calculating conditional and conjunctional false discovery rates for genetic variants that are pleiotropic for pairs of phenotypes.</p> <ol> <li>genref.zip is preprocessed information that can be directly used with the R package cfdr.pleio, available from github<br> </li> <li>genref_rawdata.zip contains raw data downloaded from the 1000 Genome projects. You only need to download this if you want to re-create or modify the preprocessed reference data from above. The original code for creating the preprocessed data is available from github.</li> </ol> <p><strong>Usage </strong></p> <p>See the instructions at the two named github repositories for details.</p> <p><strong>Credit</strong></p> <p>The code for generating the preprocessed reference data as well as some auxiliary information were forked from the MATLAB package <a href="https://github.com/precimed/pleiofdr">pleiofdr</a></p> <p>The original concept of the conditional and conjunctional FDR were described in <a href="https://doi.org/10.1371/journal.pgen.1003455">Andreassen et al. (2013)</a>. For a recent overview of methods and applications, see <a href="https://doi.org/10.1007/s00439-019-02060-2">Smeland et al. (2019).</a></p> <p> </p>
Significant eQTLs and expression TWAS reference panels (AMP-AD brain and EADB Belgian LCL cohorts)
<p>This dataset is part of the manuscript "<em><strong>New insights into the genetic etiology of Alzheimer’s disease and related dementias</strong></em>" by Bellenguez, Küçükali, et al. Nature Genetics 2022.</p> <p>Publication link: <a href="https://www.nature.com/articles/s41588-022-01024-z">https://www.nature.com/articles/s41588-022-01024-z</a></p> <p>GitHub repository of all QTL/TWAS data shared for this study: <a href="https://github.com/SleegersLab-VIBCMN/EADB_GWAS_NatureGenetics_QTL_TWAS">https://github.com/SleegersLab-VIBCMN/EADB_GWAS_NatureGenetics_QTL_TWAS</a></p> <p>For details, please see the publication. For any questions, please contact Fahri Küçükali (<a href="mailto:fahri.kucukali@uantwerpen.vib.be">fahri.kucukali@uantwerpen.vib.be</a>) and Kristel Sleegers (<a href="mailto:Kristel.Sleegers@uantwerpen.vib.be">Kristel.Sleegers@uantwerpen.vib.be</a>).</p> <p>Significant eQTL catalogues are compressed with <em>gzip </em>and tar achieve of expression TWAS reference panels are compressed with <em>bzip2</em>.</p> <p><strong>eQTL catalogues</strong></p> <p>The files show significant eQTL - gene pairs mapped in AMP-AD brain and EADB Belgian LCL cohorts. The catalogues are in hg38/GRCh38 human genome build. Most of the columns in the files are based on FastQTL output (<a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a>).</p> <p><em>eQTL file columns:</em></p> <ol> <li>variant_id - ID of the significant eQTL variant based on the dbSNPv151 rsID annotation or hg38/GRCh38 CHR_POS_REF_ALT ID if rsID not available.</li> <li>gene_id - eGene ENSG gene ID based on GENCODEv24 (AMP-AD) or GENCODEv32 (EADB Belgian)</li> <li>tss_distance - Genomic distance between eQTL variant and eGene</li> <li>ma_samples - Number of samples carrying the minor allele</li> <li>ma_count - Total count of minor alleles</li> <li>maf - Minor allele frequency</li> <li>pval_nominal - Nominal <em>P</em>-value of the association</li> <li>slope - Slope of the association with respect to alternative (ALT) allele indicated on column 14</li> <li>slope_se - Standard error of the slope</li> <li>pval_nominal_threshold - Nominal <em>P</em>-value significant threshold for this eGene</li> <li>min_pval_nominal - Most significant <em>P</em>-value observed for this eGene</li> <li>pval_beta - permutation <em>P</em>-value obtained via beta approximation and later used to calculate Storey q-values</li> <li>gene_name - eGene name based on GENCODEv24 (AMP-AD) and GENCODEv32 (EADB Belgian)</li> <li>GRCh38_chr_pos - Genomic position of the variant, separated by underscore</li> <li>ref_alt - Reference (REF) and alternative (ALT) allele of the variant, separated by ">" sign. ALT is the tested (A1) allele</li> </ol> <p>Of note, we also mapped the significant sQTLs in the same datasets (please see the data availability section of the manuscript or the GitHub repository).</p> <p><strong>Expression TWAS reference panels</strong></p> <p>Custom expression TWAS reference panels prepared using FUSION pipeline (<a href="http://gusevlab.org/projects/fusion/">http://gusevlab.org/projects/fusion/</a>) in AMP-AD brain and EADB Belgian LCL cohorts. All data in hg38/GRCh38 genome build. In each directory, you will find ".pos", ."profile", and ".profile.err" files. These are explained in the FUSION website as well, but briefly these are:</p> <ol> <li><strong>.pos:</strong> This is a position file that describes the 1Mb extended gene start and end coordinates for each calculated weight file for each gene expression phenotype. Used for scanning the variants in those coordinates for TWAS.</li> <li><strong>.profile: </strong>This informs about all prediction weights calculated, in terms of number of variants in the model, heritability information, and R2 info for each prediction model used (top1, blup, enet, bslmm, lasso; bslmm was not used therefore has NA values).</li> <li><strong>.profile.err: </strong>This summarizes the reference panel in terms of average hsq (with SD), and which model is the best performing.</li> </ol> <p>Each TWAS weight is provided in a .RDat file under <strong>All_Expression_Weights</strong>, and in this data we included all calculated functional weights independent of the fact that they are heritable features or not. In our TWAS analyses, we included the heritable functional weights at a hsq <em>P</em>-value ≤ 0.05 level.</p> <p>Please also see the splicing TWAS reference panels we prepared in the same datasets (see the data availability section of the manuscript or the GitHub repository). If you need an LD reference data in hg38/GRCh38 genome build based on 1000 Genomes NFE samples (whose variant ID annotation are matching to these functional weights), suitable for running the TWAS/FUSION pipeline, please contact us.</p>
reference
<p>references for manuscript</p>
Data from: Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway
<p>Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (<i>Cyclopterus lumpus</i> Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb, and genome annotation predicted 21,480 protein-coding genes. Genome wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of <i>AMH</i> in the Lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One <i>AMH</i> copy showed similarity to <i>AMH/AMHY</i> in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of <i>AMH</i> in Lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits Lumpfish conservation management and aquaculture.</p>
Reference datasets of SCRIP for scATAC-seq
<p>Transcription regulators and histone modifications reference for SCRIP</p> <p>SCRIP can be downloaded from <a href="http://github.com/wanglabtongji/SCRIP">https://github.com/wanglabtongji/SCRIP</a></p> <p>Curated annotation from Cistrome Data Browser</p> <p>Version: 0.0.220112</p> <p>Release date: 2022-01-12</p>
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.