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19 results for “genome release”
Data release: Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration
<p>Source data used in the publication: Berger et al. (2021) - Provisional title: 'Whole-genome sequencing of <em>Schistosoma mansoni</em> reveals extensive diversity with limited selection despite mass drug administration'. These data were used to generate all figures used in the publication and all files are organised and labelled specifically to run with the custom code that uses these data can be found at: http://doi.org/10.5281/zenodo.4975908. </p> <p><br> <strong>File descriptions:</strong></p> <p><strong>SOURCE DATA.zip - All source data for all figures. </strong></p> <p><strong>Figure 1b:</strong></p> <ul> <li>supplementary_data_9.txt - Metadata</li> </ul> <p><strong>Figure 2a&b:</strong></p> <ul> <li>207_PCA.eigenvec - PCA eigenvectors</li> <li>207_PCA.eigenval - PCA eigenvalues</li> </ul> <p><strong>Figure 2c:</strong></p> <ul> <li>autosomes.mdist - PLINK distance matrix used to build the neighbour joining phylogeny</li> </ul> <p><strong>Figure 2d:</strong></p> <ul> <li>all.pi.pixy.schools.txt - Nucleotide diversity results for each school subpopulation.</li> </ul> <p><strong>Figure 2e:</strong></p> <ul> <li>autosomes.dxy.5kb.schools.txt - Autosomal D<sub>XY</sub> results between school subpopulations. </li> <li>autosomes.fst.5kb.schools.txt - Autosomal F<sub>ST</sub> results between school subpopulations.</li> </ul> <p><strong>Figure 2f:</strong></p> <ul> <li>admixture_all.txt - ADMIXTURE results for each sample and population sizes, column 1 represents number of populations (K), columns 3-8 represent admixture values for each population. </li> </ul> <p><strong>Figure 3a, Supplementary figure 10a:</strong></p> <ul> <li>sfs.csv - Site frequency spectra (allelic proportions at each frequency bin) for each school. </li> </ul> <p><strong>Figure 3b:</strong></p> <ul> <li>TD.all.txt - Tajima's D values calculated in 5 kb windows for each school subpopulation. </li> </ul> <p><strong>Figure 4a, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.MAYUGE.IHS.ihs.out.100bins.norm.txt.zip - Normalised iHS scores for the Mayuge district parasite populations (Selscan output).</li> </ul> <p><strong>Figure 4b, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.TORORO.IHS.ihs.out.100bins.norm.txt.zip -<strong> - </strong>Normalised iHS scores for the Tororo district parasite populations (Selscan output).</li> </ul> <p><strong>Figure 4c, Supplementary figures 13-18: </strong></p> <ul> <li>ALL.MAYUGEvsTORORO.xpehh.xpehh.out.norm.txt.zip - - Normalised XP-EHH scores between Mayuge and Tororo parasite populations.</li> </ul> <p><strong>Figure 4d, Supplementary figures 13-18:</strong></p> <ul> <li>MAYUGE_TORORO_2000.windowed.weir.txt.zip - F<sub>ST</sub> values calculated between Mayuge and Tororo populations in 2kb windows. </li> </ul> <p><strong>Figure 4e, Supplementary figures 12a&c:</strong></p> <ul> <li>MAYUGE_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Mayuge populations. </li> <li>TORORO_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Kocoge populations (Tororo district).</li> </ul> <p><strong>Figure 5a:</strong></p> <ul> <li>all.pi.treat.fix.txt.zip - Nucleotide diversity results for each treatment subpopulation</li> </ul> <p><strong>Figure 5b</strong></p> <ul> <li>autosomes.dxy.5kb.treatment.txt - <strong> </strong>- Autosomal D<sub>XY</sub> results between clearance phenotype subpopulations. </li> <li>autosomes.fst.5kb.treatment.txt<strong> </strong>- Autosomal F<sub>ST</sub> results between clearance phenotype subpopulations. </li> </ul> <p><strong>Figure 5c:</strong></p> <ul> <li>fst.windows.2kb.treatment.txt.zip - F<sub>ST</sub> values for comparisons between different treatment groups (Pre-treatment, post-treatment (good clearers), post-treatment (poor clearers))</li> </ul> <p><strong>Figure 5d: </strong></p> <ul> <li>assoc_err_binary.txt.zip - Results of binary trait association between miracidia sampled from hosts with good clearance phenotypes (where treatment appeared to be highly effective) and miracidia isolated post-treatment from hosts with poor clearance phenotypes (where miracidia are potentially derived from parasites that survived treatment.</li> </ul> <p><strong>Figure 5e:</strong></p> <ul> <li>assoc_err_linear.txt.zip - - Results of linear regression genome-wide association study with the ERR estimates for all 198 samples, using the mean of the posterior ERR estimates from Crellen et al. (2016) as a quantitative trait.</li> </ul> <p><strong>Supplementary figure 1:</strong></p> <ul> <li>median.coverage.txt - Normalised depth of read coverage (column 4) calculated in 25 kb windows (columns 2&3) across all samples for all chromosomes (column 1).</li> </ul> <p><strong>Supplementary figure 2a-f: </strong></p> <ul> <li>cohort.genotyped.txt.zip - <strong> </strong>- Variant quality site values (used to inform variant site retention or removal). </li> </ul> <p><strong>Supplementary figure 2g:</strong></p> <ul> <li>hard_filtered.imiss.txt - Per sample variant missingness (used to inform quality control).</li> </ul> <p><strong>Supplementary figure 2h:</strong></p> <ul> <li>hard_filtered_filtindv.lmiss.txt.zip - Per site missingness (used to inform quality control).</li> </ul> <p><strong>Supplementary figure 3a, 4a, 4b:</strong></p> <ul> <li>prunedData.eigenvec - PCA eigenvectors</li> <li>prunedData.eigenval - PCA eigenvalues</li> </ul> <p><strong>Supplementary figure 3b:</strong></p> <ul> <li>pruned_data.mdist.csv - Distance matrix used as the basis for the neighbour joining phylogeny.</li> </ul> <p><strong>Supplementary figure 5:</strong></p> <ul> <li>cv_scores.txt - ADMIXTURE coefficient of variation scores (column 2) for each population size (1).</li> </ul> <p><strong>Supplementary figure 6:</strong></p> <ul> <li>*_SMC_SE.csv - SMC++ results (from 25 subsampled replicates) for each school subpopulation and outgroup samples. </li> </ul> <p><strong>Supplementary Figure 7:</strong></p> <ul> <li>smcpp.csv - SMC++ results for each school subpopulation and outgroup samples. </li> </ul> <p><strong>Supplementary Figure 8a-d</strong></p> <ul> <li>pi.per_host.txt.zip - Nucleotide diversity values for each host infrapopulation. </li> </ul> <p><strong>Supplementary Figure 9:</strong></p> <ul> <li>sexing.csv - inferred sex (based on differential read coverage over pseudoautosomal and Z-specific regions of the Z chromosome). </li> </ul> <p><strong>Supplementary Figure 10b:</strong></p> <ul> <li>sfs_res.csv - residuals for the SFS analysis in 3a/10a.</li> </ul> <p><strong>Supplementary Figure 11:</strong></p> <ul> <li>MAYUGE_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Mayuge population in 2kb windows. </li> <li>Tororo_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Tororo population in 2kb windows. </li> </ul> <p><strong>Supplementary Figures 13-18:</strong></p> <ul> <li>genes.bed - Coordinates of gene models (<em>S. mansoni </em>v7 annotation).</li> <li>KOCOGE_SITE_PI.sites.pi.txt.zip - Per site nucleotide diversity values</li> <li>MAYUGE_TORORO_sites.weir.fst.txt.zip - Per site F<sub>ST</sub> values between Mayuge and Tororo populations. </li> <li>coverage_5kb.windows.txt.zip - Per sample depth of read coverage in 5 kb windows. Columns 4,5,6 represent the median, mean and sstev of coverage for each 5kb window (columns 2&3) along each chromosome (column 1). </li> <li>median.sample.coverage.txt - Median chromosomal depth of read coverage for each sample. </li> </ul> <p><strong>Supplementary Figure 19:</strong></p> <ul> <li>kocoge_median.ld.txt.zip - <strong> </strong>- The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Kocoge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> <li>mayuge_median.ld.txt.zip - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Mayuge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. </li> </ul> <p><strong>Misc files:</strong></p> <p>schools.list - List of samples and schools where they were sampled. </p> <p> </p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
<p>Phenotypic reaction norms are often shaped and constrained by selection and are important for allowing organisms to respond to environmental change. However, selection cannot constrain reaction norms for environmental conditions that populations have not experienced. This may allow cryptic neutral genetic variation for the reaction norm to accumulate such that a release of phenotypic variation occurs when it is exposed to novel conditions. Most genomic diversity behaves as if functionally neutral. Genome-wide diversity metrics may therefore correlate with levels of cryptic genetic variation and, as a result, could exhibit a positive relationship with a release of phenotypic variation in novel environments. To test this hypothesis, we conducted translocations of juvenile brook trout (Salvelinus fontinalis) from 12 populations to novel uninhabited ponds that represented a gradient of environmental conditions. We assessed reaction norms for morphological traits (body size and four morphometric relative warps) across pond environmental gradients and evaluated the effect of genome-wide heterozygosity on phenotypic variability. All traits displayed plastic reaction norms. Overall, we found some evidence that a release of phenotypic variation consistent with cryptic genetic variation can occur in novel environmental conditions. However, the extent to which this release was correlated with average genome-wide diversity was limited to only one of five morphological traits examined. Our results suggest that the link between genomic diversity and the accumulation of cryptic genetic variation in reaction norms may be limited. Similarly, reaction norms were constrained for many of the morphological traits examined. Past conditions may have constrained reaction norms in the putatively novel environments despite significant deviations from contemporary source population habitat. Additionally, as a generalist colonizing species brook trout may exhibit plastic phenotypes across a wide range of environmental conditions.</p>
bacteria_genomic_rates_data: First release
<p>This is the first release of the data used for: Genomic rates of evolution in bacteria</p>
Data release: Genomic evidence of contemporary hybridization between Schistosoma species
<p>This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see https://www.sanger.ac.uk/about/who-we-are/research-policies/open-access-science/</p> <p>Please contact Duncan Berger (db22@sanger.ac.uk) with questions regarding pre-publication use of this dataset. </p> <p>SchCurr1.primary.fa - <em>Schistosoma curassoni</em> primary genome assembly </p> <p>SchCurr1.haplotypes.fa - Haplotype variants (unphased from SchCurr1.primary.fa)</p> <p>SchCurr1.primary.fa.tbl - RepeatMasker2 output (run on the primary assembly).</p> <p>allchrs.vcf.gz - All variants called on chromosomes 1-7+Z (Post quality control, with the exception that variants found within repetitive regions are included)</p> <p>MITO.vcf.gz - All mitochondrial variants. </p> <p>SchCurr1.genomethreader.gff3 - Genomethreader based gene structure predictions (based on spliced alignments of <em>S. mansoni</em> (v9) transcript and protein sequences). </p>
The history of chromosomal instability in genome doubled tumors : Data release
<p>Released data for '<em>The history of chromosomal instability in genome doubled tumors</em>'.</p>
Genome Release: Vitis vinifera cv. Dakapo v1
<p>Genome assembly and annotations of the Dakapo variety of grapevine (<em>Vitis vinifera </em>L.).</p>
Data From: Evaluating the correlation between genome-wide diversity and the release of plastic phenotypic variation in experimental translocations to novel natural environments
Open the record for dataset details and reuse information.
Supplementary material 1 from: Zúñiga JD, Gostel MR, Mulcahy DG, Barker K, Hill A, Sedaghatpour M, Vo SQ, Funk VA, Coddington JA (2017) Data Release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution. PhytoKeys 88: 119-122. https://doi.org/10.3897/phytokeys.88.14607
List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers. All the sequences are included in the GGI-Gardens BioProject. : Explanation note: List of samples collected for the Global Genome Initiative for Gardens project selected for DNA barcoding, with GenBank accession numbers and genetic sample identification numbers.
Grapegenomics.com - Genome release: Vitis interspecific cross - Rubired cl. FPS02 - chromosome scale
<p><a href="https://www.grapegenomics.com/pages/VRubired/">https://www.grapegenomics.com/pages/VRubired/</a></p>
MCM2-7 loading-dependent ORC release ensures genome-wide origin licensing
GEO Series GSE240779. Saccharomyces cerevisiae. 44 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release
GEO Series GSE216974. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [PRO-seq]
GEO Series GSE278359. Homo sapiens. 6 samples. Type: Other.
SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells
GEO Series GSE278364. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing; Other.
SF3B1 K700E Mutation Induces Genome-Wide Enhancement of Transcriptional Pause Release in ES Cells [RNA-seq]
GEO Series GSE278363. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Physiological and genomic analysis of Saccharomyces cerevisiae artificial hybrids with improved fermentation performance and mannoprotein release capacity
GEO Series GSE48117. Saccharomyces cerevisiae. 3 samples. Type: Genome variation profiling by array.
Grapegenomics.com - Genome release: Vitis vinifera cv. Muscat of Alexandria cl. FPS02
<p><a href="https://www.grapegenomics.com/pages/VvMuscAlex/">https://www.grapegenomics.com/pages/VvMuscAlex/</a></p> <p> </p> <p>Funding:</p> <p>Specialty Crop Research Initiative Competitive Grant, Award No. <a target="_blank" rel="noreferrer noopener">2022-51181-38240</a>, of the USDA National Institute of Food and Agriculture and E.J. Gallo Winery</p>
Grapegenomics.com - Genome release: Vitis vinifera cv. Muscat of Alexandria cl. FPS02 (pseudomolecules)
<p>https://www.grapegenomics.com/pages/VvMuscAlex/pseudomolecules_v1.0</p> <p> </p> <p>Funding:</p> <p><span>Specialty Crop Research Initiative Competitive Grant, Award No. <a target="_blank" rel="noreferrer noopener">2022-51181-38240</a>, of the USDA National Institute of Food and Agriculture and E.J. Gallo Winery</span></p>
Grapegenomics.com - Genome release: Planococcus ficus VMBCA21f
<p><a href="https://www.grapegenomics.com/pages/Pficus/">https://www.grapegenomics.com/pages/Pficus/</a></p>
Genomic Response of Escherichia coli during coexpression of a bacteriocin release protein
GEO Series GSE16946. Escherichia coli K-12; Escherichia coli. 9 samples. Type: Expression profiling by array.
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