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470 results for “Analysis of Variation”
Data to reproduce analysis in "Systematic analysis of transcriptional and epigenetic effects of genetic variation in Kupffer cells enables discrimination of cell intrinsic and environment-dependent mechanisms"
<p>Here you can find the datasets necessary to reproduce all analyses described in the Glass lab paper by <a href="https://www.biorxiv.org/content/10.1101/2022.09.22.509046v1">Bennett et al</a>. The python and R code for reproducing analysis and figures can be found on our linked <a href="https://github.com/HunterBennett/KupfferCell_NaturalGeneticVariation">github repository.</a></p> <p>Briefly, this paper explores the effect of natural genetic variation <em>in vivo</em>, using Kupffer cells as a model cell type. We collect and analyze transcriptional and epigenetic data (ATAC-seq, H3K27Ac ChIP-seq) to identify putative <em>trans</em> regulators driving differential gene expression across inbred strains of mice. Additionally, we provide evidence that <em>trans</em> effects control a majority of strain differential genes at homeostasis while <em>cis</em> effects dominate the transcriptional response to an external signal (lipopolysaccharide).</p> <p>References:</p> <p>Hunter Bennett, Ty D. Troutman, Enchen Zhou, Nathanael J. Spann, Verena M. Link, Jason S. Seidman, Christian K. Nickl, Yohei Abe, Mashito Sakai, Martina P. Pasillas, Justin M. Marlman, Carlos Guzman, Mojgan Hosseini, Bernd Schnabl, Christopher K. Glass bioRxiv 2022.09.22.509046; doi: <a href="https://doi.org/10.1101/2022.09.22.509046">https://doi.org/10.1101/2022.09.22.509046</a></p> <p> </p>
R Code and Re-analyzed Datasets for: Robust approaches for the quantitative analysis of genome formula variation in multipartite and segmented viruses
<p>This submission includes all the scripts and data analyzed in the manuscript "Robust approaches for the quantitative analysis of genome formula variation in multipartite and segmented viruses". This manuscript is a technical note on how genome formula data can be analyzed. There are no new experimental data in the manuscript, as published datasets are re-analyzed. Here we reproduce those datasets as formatted for our analysis, for the convenience of the reader. Please consult the README.txt file first.</p> <p>The corresponding paper was published in Viruses <em>16</em>(2): 270. (<a href="https://doi.org/10.3390/v16020270">https://doi.org/10.3390/v16020270</a>).</p> <p>This is the second version of the code, corresponding to the final version of the paper. The intial restricted version for review had a DOI 10.5281/zenodo.10355273.</p> <p> </p>
Variation in Detected Adverse Events using Trigger Tools: A Systematic Review and Meta-Analysis
<p>Raw data sets for the meta-analysis.</p> <p>Data collection file with all the information extracted from the included studies.</p> <p>QAT file with the information from the quality assessment tool (QAT) for all included studies.</p> <p>ReadMe with information on data sets and updates.</p> <p>Codebooks for both data sets.</p>
Intraspecific variation in the sensitivity of bees to pesticides: a comparative analysis in Bombus terrestris and Osmia bicornis
<p>These files describe the archived CSV files associated with the publication "Intra-specific variation in sensitivity of Bombus terrestris and Osmia bicornis to three pesticides"</p> <p>By Alberto Linguadoca, Margret Jürison, Sara Hellström, Edward A. Straw1, Peter Šima, Reet Karise, Cecilia Costa, Giorgia Serra, Roberto Colombo, Robert J. Paxton, Marika Mänd, Mark J. F. Brown<br> </p>
Assessing Quality Variations in Early Career Researchers' Data Management Plans: Quantitative Data of the Content Analysis
<p>The data includes the numerical results of the ranking of the data management plans created during the Basics of Research Data Management (BRDM) courses worth 3 ECTS credits in the years 2020 - 2022. The ranking was made using the Finnish DMP Evaluation Guidance (https://doi.org/10.5281/zenodo.4729831). Additionally, the data contains the results of the analysis of the best RDM practices included in the DMPs.</p> <p>Note 1: The comma-separated coded CSV version 1 (5.2.2024) may not open correctly on MacOS. You can use the comma-delimited CSV file version 2 or 3 (31.5.2024).</p> <p>Note 2: Versions 1 (Quality_variations_in_ECRs_DMPs_data) and 3 (Quality_variations_in_ECRs_DMPs_data_ver_3) contain evaluations of DMPs, best practices for data management, as well as methods for data sharing, storage, and preservation. In version 2 (Quality_variations_in_ECRs_DMPs_data_ver_2), the methods for data sharing, storage, and preservation are missing.</p> <p>Data is related to the research article https://doi.org/10.2218/ijdc.v18i1.873.</p>
Sample data for analysis of sequence variation in HIV
<p>These are downsampled interleaved paired fastq datasets from Jair et. 2019 (<a href="https://doi.org/10.1371/journal.pone.0214820">https://doi.org/10.1371/journal.pone.0214820</a>). The datasets were prepared by:</p> <ol> <li>Downloading original data from NCBI SRA (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517147)</li> <li>Trimming contaminating Nextera adapters using trim-galore</li> <li>Mapping reads against nxb2 reference of HIV genome (K03455.1) with BWA MEM</li> <li>Restricting mapped reads to <em>pol</em> gene vicinity (K03455.1:2000-5100)</li> <li>Downsampling mapped data to ~10% of the original with Picard's DownsampleSam</li> <li>Converting BAM to Interleaved Fastq with Picard's SamToFastq</li> <li>Gzipping resultant interleaved paired fastq files</li> </ol>
Characteristic and spatiotemporal variation of air pollution in Northern China based on correlation analysis and clustering analysis of five air pollutants
<p>original daily data for 'Characteristic and spatiotemporal variation of air pollution in Northern China based on correlation analysis and clustering analysis of five air pollutants'</p>
Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture
<p>Anterior cruciate ligament (ACL) rupture is an important condition of the human knee. Second ruptures are common and societal costs are substantial. Canine cranial cruciate ligament (CCL) rupture closely models the human disease. CCL rupture is common in the Labrador Retriever (5.79% prevalence), ~100-fold more prevalent than in humans. Labrador Retriever CCL rupture is a polygenic complex disease, based on genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers. Dissection of genetic variation in complex traits can be enhanced by studying structural variation, including copy number variants (CNVs). Dogs are an ideal model for CNV research because of reduced genetic variability within breeds and extensive phenotypic diversity across breeds. We studied the genetic etiology of CCL rupture by association analysis of CNV regions (CNVRs) using 110 case and 164 control Labrador Retrievers. CNVs were called from SNPs using three different programs (PennCNV, CNVPartition, and QuantiSNP). After quality control, CNV calls were combined to create CNVRs using ParseCNV and an association analysis was performed. We found no strong effect CNVRs but found 46 small effect (max(T) permutation P<0.05) CCL rupture associated CNVRs in 22 autosomes; 25 were deletions and 21 were duplications. Of the 46 CCL rupture associated CNVRs, we identified 39 unique regions. Thirty four were identified by a single calling algorithm, 3 were identified by two calling algorithms, and 2 were identified by all three algorithms. For 42 of the associated CNVRs, frequency in the population was <10% while 4 occurred at a frequency in the population ranging from 10-25%. Average CNVR length was 198,872bp and CNVRs covered 0.11 to 0.15% of the genome. All CNVRs were associated with case status. CNVRs did not overlap previous canine CCL rupture risk loci identified by GWAS. Associated CNVRs contained 152 annotated genes; 12 CNVRs did not have genes mapped to CanFam3.1. Using pathway analysis, a cluster of 19 homeobox domain transcript regulator genes was associated with CCL rupture (P=6.6E-13). This gene cluster influences cranial-caudal body pattern formation during embryonic limb development. Clustered genes were found in 3 CNVRs on chromosome 14 (HoxA), 28 (NKX6-2), and 36 (HoxD). When analysis was limited to deletion CNVRs, the association was strengthened (P=8.7E-16). This study suggests a component of the polygenic risk of CCL rupture in Labrador Retrievers is associated with small effect CNVs and may include aspects of stifle morphology regulated by homeobox domain transcript regulator genes.</p>
Repository for adjoint convolution analysis of sea level variations near Charleston and Nantucket
<p>This repository contains adjoint sensitivity, forcing, and example adjoint-convolution script to reconstruct sea level variations near Charleston and Nantucket. </p>
Figure 78 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 78. Bemisia afer complex, Madeira, Santana, Faja do Niguiera, 15-XII-92, ex. Myrica toya, F. Aguiar, coll.
Figure 77 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 77. Bemisia afer complex, Madeira, Faja do Penedo, 20.iii.92, ex. Marcetella madeirensis, F. Aguiar, coll., #C136.
Figure 79 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 79. Bemisia afer complex, Madeira, Levada above Ribeiro Bonita, nr. Sao Jorge Icod de los Vinos, 01 Apr. 1995, ex. Sibthorpia peregrina (Scrophulariaceae), J. Martin and A. Aguiar, colls., JHM # 6590.
Figure 76 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 76. Bemisia afer complex, Madeira, Faja do Penedo, 20-iii-1992, ex. Marcetella madeirensis, F. Aguiar, coll. # C136.
Figure 71 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 71. Bemisia afer complex, Canary Islands, Tenerife, Barranco de las Moradas, ex. Eschium sp., J. Martin, coll., JHM # 7048.
Figure 70 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 70. Bemisia afer complex, Canary Islands, Tenerife, Barranco de los Moradas, nr. Icod de los Vinos, approx 700-900 m., 18 May 1997, ex Rubus fruticosus grp., J.H. Martin, coll., JHM #7047.
Figure 69 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 69. Bemisia afer complex, Canary Islands, La Palma, Ctr. Barbuento, ex. Rubus sp., 21-VI-1997, E. Hernandez-Suarez, coll.
Figure 68 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 68. Bemisia afer complex, Canary Islands, Tenerife, Barranco, de las, Moradas, nr., Icod de los Vinos, at 7-900m, 18 May 1997, ex. Cistus sp., J. Martin, coll., JHM # 7046.
Figure 67 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 67. Bemisia afer complex, Canary Islands, Tenerife: Guimar, Bco de Badajos, 25 Nov. 2000, ex. Bencomia caudata, -upper surfaces, J.H.Martin, coll.
Figure 74 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 74. Bemisia afer complex, Madeira, Seixal, 6-III-92, ex. Ocotea foetens., (Lauraceae), F. Aguiar, coll. #C125.
Figure 75 in A preliminary report on the World species of Bemisia Quaintance and Baker and its congeners (Hemiptera: Aleyrodidae) with a comparative analysis of morphological variation and its role in the recognition of species Raymond Gill
Figure 75. Bemisia afer complex, Madeira, Levado do Norte,, Below Bica da Cana, 1000-1100 m, 16 May 1997, ex. Clethra arborea, J.H. Martin coll. #7040. This illustration is less detailed than others, and is meant only to show general body shape and setal patterns.
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.