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52 results for “strain mapping”
Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.
<p>This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.</p> <p>The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. </p> <p>The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP<sup>S</sup> = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP<sup>A</sup>-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.</p> <p> </p>
Data set for Microscale and nanoscale strain mapping techniques applied to creep of rocks
<p>Data set (figures and data involved in their making) for Quintanilla-Terminel, A., M. E. Zimmerman, B. Evans, and D.L. Kohlstedt, Microscale and nanoscale strain mapping techniques applied to creep of rocks, Solid Earth Discuss., https://doi.org/10.5194/se-2017-27, in review, 2017.</p>
Aladdin: High-Resolution Maps of Left Atrial Displacements and Strains Estimated with 3D Cine MRI
<p>The uploaded files include high-resolution 3D images of the left atrium from 18 individuals—10 healthy volunteers and 8 patients with various cardiovascular diseases—along with their corresponding left atrium segmentation maps. Additionally, a deformation atlas based on the 10 healthy cases is also provided.</p> <p>For more information, visit: <a href="https://github.com/cgalaz01/aladdin_cmr_la" target="_new" rel="noopener">https://github.com/cgalaz01/aladdin_cmr_la</a></p>
Data in support of: `Two-Dimensional Strain Mapping with Scanning Precession Electron Diffraction: An Investigation into Data Analysis Routines'
<p>This upload contains data in support of a manuscript currently under review. More details to follow.</p>
Fibronectin-Based Nanomechanical Biosensors to Map 3D Surface Strains in Live Cells and Tissue (Raw Data)
<p>This is the raw microscope imaging data for the manuscript titled "Fibronectin-Based Nanomechanical Biosensors to Map 3D Surface Strains in Live Cells and Tissue."</p>
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
Mapped ATAC-seq data for mock and HSV-1 strain 17 infection and infection with null mutants of HSV-1
<p>Sample annotation:</p> <table> <tbody> <tr> <td>Mock_1</td> <td>mock infection, replicate 1</td> </tr> <tr> <td>Mock_2</td> <td>mock infection, replicate 2</td> </tr> <tr> <td>WT_1</td> <td>HSV-1 wt, strain 17, replicate 1</td> </tr> <tr> <td>WT_2</td> <td>HSV-1 wt, strain 17, replicate 2</td> </tr> <tr> <td>WT_plus_PAA_1</td> <td>HSV-1 wt, strain 17, +PAA, replicate 1</td> </tr> <tr> <td>WT_plus_PAA_2</td> <td>HSV-1 wt, strain 17, +PAA, replicate 2</td> </tr> <tr> <td>dICP0_1</td> <td>HSV-1 lacking expression of ICP0, replicate 1</td> </tr> <tr> <td>dICP0_2</td> <td>HSV-1 lacking expression of ICP0, replicate 2</td> </tr> <tr> <td>dICP22_1</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 1</td> </tr> <tr> <td>dICP22_2</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 2</td> </tr> <tr> <td>dICP22_3</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 3</td> </tr> <tr> <td>dICP22_4</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, replicate 4</td> </tr> <tr> <td>dICP22_plus_PAA_1</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, +PAA, replicate 1</td> </tr> <tr> <td>dICP22_plus_PAA_2</td> <td>HSV-1 lacking expression of ICP22, HSV-1 strain F mutant R325, +PAA, replicate 2</td> </tr> <tr> <td>dICP27_1</td> <td>HSV-1 lacking expression of ICP27, KOS, replicate 1</td> </tr> <tr> <td>dICP27_2</td> <td>HSV-1 lacking expression of ICP27, KOS, replicate 2</td> </tr> <tr> <td>dVHS_1</td> <td>HSV-1 lacking expression of UL41, replicate 1</td> </tr> <tr> <td>dVHS_2</td> <td>HSV-1 lacking expression of UL41, replicate 2</td> </tr> </tbody> </table>
Anthracycline Induced Cardiotoxicity - Early Detection by Combination of Diastolic Strain and T2-mapping
ClinicalTrials.gov study NCT03940625. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Strain Mapping of Two-Dimensional Heterostructures with Subpicometer Precision
<p>The sample is a WS<sub>2</sub>-WSe<sub>2</sub> lateral heterojunction with an in-plane epitaxial interface. The datasets were collected by electron microscope pixel array detector (EMPAD) under the condition described in this paper (Han, et al. Nano Letters, 18, 3746-3751 (2018)). The rotation angle between the real space and diffraction space in these datasets is 15 degrees. The data have also been analyzed in our recent paper (arXiv:2111.06496) and a conference proceeding (Shi, et al. Microsc. Microanal. 27 Suppl 1, 2021). </p>
Data from: Mapping QTL contributing to variation in posterior lobe morphology between strains of Drosophila melanogaster
Closely-related, and otherwise morphologically similar insect species frequently show striking divergence in the shape and/or size of male genital structures, a phenomenon thought to be driven by sexual selection. Comparative interspecific studies can help elucidate the evolutionary forces acting on genital structures to drive this rapid differentiation. However, genetic dissection of sexual trait divergence between species is frequently hampered by the difficulty generating interspecific recombinants. Intraspecific variation can be leveraged to investigate the genetics of rapidly-evolving sexual traits, and here we carry out a genetic analysis of variation in the posterior lobe within D. melanogaster. The lobe is a male-specific process emerging from the genital arch of D. melanogaster and three closely-related species, is essential for copulation, and shows radical divergence in form across species. There is also abundant variation within species in the shape and size of the lobe, and while this variation is considerably more subtle than that seen among species, it nonetheless provides the raw material for QTL mapping. We created an advanced intercross population from a pair of phenotypically-different inbred strains, and after phenotyping and genotyping-by-sequencing the recombinants, mapped several QTL contributing to various measures of lobe morphology. The additional generations of crossing over in our mapping population led to QTL intervals that are smaller than is typical for an F2 mapping design. The intervals we map overlap with a pair of lobe QTL we previously identified in an independent mapping cross, potentially suggesting a level of shared genetic control of trait variation. Our QTL additionally implicate a suite of genes that have been shown to contribute to the development of the posterior lobe. These loci are strong candidates to harbor naturally-segregating sites contributing to phenotypic variation within D. melanogaster, and may also be those contributing to divergence in lobe morphology between species.
Combined Study of ATrial Strain and Voltage by High Density Mapping in Young Patients With Atrial Fibrillation.
ClinicalTrials.gov study NCT05565183. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: Mapping QTL contributing to variation in posterior lobe morphology between strains of Drosophila melanogaster
Open the record for dataset details and reuse information.
Genome-wide mapping of transcription start sites in a ∆set2 strain
GEO Series GSE62735. Saccharomyces cerevisiae. 4 samples. Type: Other.
ssDNA mapping in dmc1 strains
GEO Series GSE30071. Saccharomyces cerevisiae. 12 samples. Type: Genome variation profiling by genome tiling array.
Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains
GEO Series GSE77217. Bacillus subtilis. 7 samples. Type: Expression profiling by high throughput sequencing.
Mutation Mapping of 40 Streptococcus suis strains
GEO Series GSE40035. Streptococcus suis. 80 samples. Type: Genome variation profiling by genome tiling array.
Genome-wide mapping of H3K4 tri-methylation in ΔUvkmt2 mutant strain of Ustilaginoidea virens
GEO Series GSE203326. Ustilaginoidea virens. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Whole-genome nucleosome mapping in meiotic diploid Saccharomyces species (S. paradoxus, S. mikatae, S. kudriavzevii) and wild-derived S. cerevisiae strains (YPS128, UWOPS03-461.4)
GEO Series GSE71929. Saccharomyces paradoxus; Saccharomyces cerevisiae; Saccharomyces kudriavzevii; Saccharomyces mikatae. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Nucleosome position mapping by micrococcal nuclease analysis in S. cerevisiae of Top1-AID/Top2-AID strains with auxin in galactose-rich media
GEO Series GSE196945. Saccharomyces cerevisiae. 11 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide maps of nucleosome positions in Saccharomyces strains bearing heterologous DNA on yeast artificial chromosomes
GEO Series GSE39011. Saccharomyces cerevisiae. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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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.