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3,458 results for “Chromosomes”
The Chromosome 19 miRNA Cluster Guards Trophoblasts Against Overacting Innate Immunity
GEO Series GSE293705. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Chromosomal status of GM00285 and GM05563 fibroblast and iPSCs
GEO Series GSE52585. Homo sapiens. 5 samples. Type: Genome variation profiling by SNP array; Genome variation profiling by genome tiling array.
Figure 3 from: Astuti G, Bartolucci F, Bernardo L, Conti F, Peruzzi L (2019) Chromosome numbers for the Italian flora: 8. Italian Botanist 8: 117-121. https://doi.org/10.3897/italianbotanist.8.49156
Figure 3 Poa ligulata Boiss., 2n = 14. Scale bar: 10 μm.
Figure 1 from: Astuti G, Bartolucci F, Bernardo L, Conti F, Peruzzi L (2019) Chromosome numbers for the Italian flora: 8. Italian Botanist 8: 117-121. https://doi.org/10.3897/italianbotanist.8.49156
Figure 1 Centaurea subtilis Bertol., 2n = 22. Scale bar: 10 μm.
Supplementary data for human Y-chromosome gene expression analysis
<p>Processed data for:</p> <p>AK Godfrey, S Naqvi, L Chmátal, JM Chick, RN Mitchell, SP Gygi, H Skaletsky, DC Page. Quantitative analysis of Y-chromosome gene expression across 36 human tissues. <em>Genome Res</em> (2020).</p> <p>The following six files are provided for reference and for use in future analyses.</p> <p>(1) <strong>gencode.v24.annotation.basic_ccds_nopar.gtf.gz</strong> — transcriptome annotation used in analyses</p> <p>(2) <strong>gtex.ksto.gen24c.prefilt_pass1.genes.est_counts.txt.gz</strong> — genes x samples matrix containing estimated count values output by kallisto for all samples passing initial set of metadata-based filters.</p> <p>(3) <strong>gtex.ksto.gen24c.prefilt_pass1.pcgenes.tpm.txt.gz</strong> — protein-coding genes x samples matrix containing TPM values output by kallisto for all samples passing initial set of metadata-based filters. </p> <p>(4) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.tpm.txt.gz </strong>— protein-coding genes x samples matrix containing TPM values output by kallisto for samples passing initial metadata-based filters and expression-outlier filters.</p> <p>(5) <strong>gtex.ksto.gen24c.prefilt_pass1.postfilt_pass.pcgenes.adj_tpm.txt.gz </strong>— protein-coding genes x samples matrix (based on file #4 above) containing TPM values adjusted for RIN, ischemic time, and intronic-read mapping rate.</p> <p>(6) <strong>gtex_metadata_subset.txt</strong> — sample/donor metadata</p> <p>The remaining 24 files contain the input data required to replicate analyses in the manuscript, as detailed at <a href="https://github.com/akg8/MSY-expression">https://github.com/akg8/MSY-expression</a>. HDF5 (`.h5`) files contain individual <a href="https://pandas.pydata.org">pandas</a> DataFrame objects with the key `df`. These files can be downloaded individually, or they can be downloaded all at once by downloading the file <strong>msy_expression.all_input_data.zip </strong>(recommended).</p> <p>---</p> <p><strong>Version history:</strong></p> <ul> <li><strong>Version 1</strong> contained just the six listed files above.</li> <li>In <strong>Version 2</strong>, the remaining 24 files needed for reproducing analyses were added. In addition, gtex_metadata_subset.txt was updated with the previously missing column `SEX`.</li> <li>In <strong>Version 3</strong>, a single zipped file msy_expression.all_input_data.zip was added so that all input data for re-analysis can be downloaded more conveniently.</li> </ul>
Figure 6 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973
Figure 6 Pulmonaria hirta L. from Parco di Monte Paderno (Bologna), 2n = 22. Scale bar: 10 μm.
Figure 5 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973
Figure 5 Pulmonaria hirta L. from Parco di Monte Paderno (Bologna), 2n = 28. Scale bar: 10 μm.
Figure 9 from: Astuti G, Bedini G, Ciccarelli D, Liu L, Tiburtini M, Peruzzi L (2020) Chromosome numbers for the Italian flora: 9. Italian Botanist 9: 101-110. https://doi.org/10.3897/italianbotanist.9.54973
Figure 9 Stachys thirkei K.Koch, 2n = 30 from Monte Rosato (Fermo). Scale bar: 10 μm.
Chromosome-level genome assembly of Chinese mitten crab (Eriocheir japonica sinensis)
<p>The Chinese mitten crab (<i>Eriocheir japonica sinensis</i>) is one of the most popular breeding species of crab in China due to its high economic and nutritional value. However, earlier published genome assemblies of <i>E. j. sinensis</i> have been highly fragmented due to limited sequencing and assembly techniques.<b> </b>In this study, we performed high-coverage sequencing of the Chinese mitten crab using advanced high-through chromosome conformation capture (Hi-C) technology and anchored these Hi-C data to previously published contig-level genome assembly for chromosome construction. Thus, we successfully assembled the first chromosome-level reference genome of <i>E. j. sinensis</i>, which contained 72 chromosomes with a N50 length of 17.61 Mb. Evaluation results demonstrated a high degree of genomic connectivity and accuracy. Acquisition of the chromosome-level genome of <i>E. j. sinensis </i>not only provides a basis for the study of adaptive evolution in crabs by comparative genomics, but should also help in studies on the growth, development, and reproduction of the Chinese mitten crab.</p>
The sequence, structure, and evolution of chromosome 8
<p>This repository contains raw Strand-seq data from the CHM13 genome aligned to the CHM13 whole-genome assembly containing the telomere-to-telomere sequence of chromosome 8. These alignments were used to detect inversions in the study "The sequence, function, and evolution of a complete human chromosome 8".</p> <p>See Methods section of the above mentioned paper for more details.</p>
Figure 6 from: Di Pietro R, Conte AL, Fortini P, D'Amato G, Astuti G (2020) Chromosome numbers for the Italian flora: 10. Italian Botanist 10: 113-122. https://doi.org/10.3897/italianbotanist.10.61847
Figure 6 Sesleria nitida Ten. from Pian de Valli (Vazia, Rieti), 2n = 28. Scale bar: 10 µm.
Figure 4 from: Di Pietro R, Conte AL, Fortini P, D'Amato G, Astuti G (2020) Chromosome numbers for the Italian flora: 10. Italian Botanist 10: 113-122. https://doi.org/10.3897/italianbotanist.10.61847
Figure 4 Plantago subulata L. from Torre dell'Orso (Melendugno, Lecce), 2n = 12. Scale bar: 10 µm.
Data from: Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits
Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex linked genetic variance (h2z). Out of 17 traits examined, eight showed a non-zero h2Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak colour in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex linked genetic variance. Sexually selected traits did not show higher h2Z than morphological traits and there was only a weak positive relationship between h2Z and sexual dimorphism. However, given the relative scarcity of empirical studies it is premature to make conclusions about the role sex chromosome linkage in the evolution of sexual dimorphism.
Data from: The fate of W chromosomes in hybrids between wild silkmoths, Samia cynthia ssp.: no role in sex determination and reproduction
Moths and butterflies (Lepidoptera) have sex chromosome systems with female heterogamety (WZ/ZZ or derived variants). The maternally inherited W chromosome is known to determine female sex in the silkworm, Bombyx mori. However, little is known about the role of W chromosome in other lepidopteran species. Here we describe two forms of the W chromosome, W and neo-W, that are transmitted to both sexes in offspring of hybrids from reciprocal crosses between subspecies of wild silkmoths, Samia cynthia. We performed crosses between S. c. pryeri (2n=28, WZ/ZZ) and S. c. walkeri (2n=26, neo-Wneo-Z/neo-Zneo-Z) and examined fitness and sex chromosome constitution in their hybrids. The F1 hybrids of both reciprocal crosses had reduced fertility. Fluorescence in situ hybridization revealed not only the expected sex chromosome constitutions in the backcross and F2 hybrids of both sexes but also females without the W (or neo-W) chromosome and males carrying the W (or neo-W) chromosome. Furthermore, crosses between the F2 hybrids revealed no association between the presence or absence of W (or neo-W) chromosome and variations in the hatchability of their eggs. Our results clearly suggest that the W (or neo-W) chromosome of S. cynthia ssp. plays no role in sex determination and reproduction, and thus does not contribute to the formation of reproductive barriers between different subspecies.
Data from: Severity of mitral valve degeneration is associated with chromosome 15 loci in Whippet dogs
Mitral valve degeneration (MVD) is the most common form of heart disease in dogs, frequently leading to left-sided congestive heart failure and cardiac mortality. Although breed-specific disease characteristics and overrepresentation point towards a genetic origin for MVD, a causative mutation and complete molecular pathogenesis are unknown. Whippet dogs are overrepresented in incidence of MVD, suggesting an inherited component in this breed. Expressivity of this condition is variable with some dogs showing evidence of more severe disease at earlier ages than other dogs. This phenomenon makes a traditional case versus control genetic study prone to phenotyping error. This study sought to avoid these common pitfalls by identifying genetic loci associated with severity of MVD in Whippets through a genome-wide association study (GWAS). 138 Whippet dogs were characterized for MVD by echocardiographic examination and a novel disease severity score was developed and adjusted for age in each subject. Single nucleotide polymorphism (SNP) genotype data (170k Illumina CanineHD SnpChip) was obtained for DNA isolated from blood of each study subject. Continuous variable genome wide association was performed after correction for population stratification by efficient mixed model association expedited (EMMAX) in 130 dogs. A genome wide significant association was identified on chromosome 15 (peak locus 57,770,326; Padj = 0.049) and secondary loci of suggestive association were identified on chromosome 2 (peak locus 37,628,875; Padj = 0.079). Positional candidate genes were identified within the primary and secondary loci including follistatin-related protein 5 precursor (FSTL5) and Rho GTPase-activating protein 26 (ARHGAP26). These results support the hypothesis that severity of MVD in whippets has a genetic basis and warrants further study by either candidate gene sequencing or next-generation techniques.
Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both X-linked and Y-linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X- and Y-centers always coincide strictly. X-autosome and Y-autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex-linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.
Data from: A simple biophysical model emulates budding yeast chromosome condensation
Mitotic chromosomes were one of the first cell biological structures to be described, yet their molecular architecture remains poorly understood. We have devised a simple biophysical model of a 300 kb-long nucleosome chain, the size of a budding yeast chromosome, constrained by interactions between binding sites of the chromosomal condensin complex, a key component of interphase and mitotic chromosomes. Comparisons of computational and experimental (4C) interaction maps, and other biophysical features, allow us to predict a mode of condensin action. Stochastic condensin-mediated pairwise interactions along the nucleosome chain generate native-like chromosome features and recapitulate chromosome compaction and individualization during mitotic condensation. Higher order interactions between condensin binding sites explain the data less well. Our results suggest that basic assumptions about chromatin behavior go a long way to explain chromosome architecture and are able to generate a molecular model of what the inside of a chromosome is likely to look like.
Emergence of Supercoiling-Mediated Regulatory Networks through the Evolution of Bacterial Chromosome Organization: Supplementary Material
<p>Data generated using <a href="https://gitlab.inria.fr/tgrohens/evotsc">EvoTSC</a> and used in the Supplementary Material to the upcoming PLOS computational biology paper.</p>
Figure 8 from: Astuti G, Bagella S, Bajona E, Barone G, Becca G, Caria MC, Di Gristina E, Fainelli F, Franzoni J, Giacò A, Orsenigo S, Paliy M, Rivieccio G, Urbani M, Peruzzi L (2023) Chromosome numbers for the Italian flora: 13. Italian Botanist 16: 135-148. https://doi.org/10.3897/italianbotanist.16.116700
Figure 8 Illecebrum verticillatum L. from Prato Rosello (Toscana), 2n = 10. Scale bar: 10 μm.
Figure 9 from: Astuti G, Bagella S, Bajona E, Barone G, Becca G, Caria MC, Di Gristina E, Fainelli F, Franzoni J, Giacò A, Orsenigo S, Paliy M, Rivieccio G, Urbani M, Peruzzi L (2023) Chromosome numbers for the Italian flora: 13. Italian Botanist 16: 135-148. https://doi.org/10.3897/italianbotanist.16.116700
Figure 9 Crupina vulgaris Cass. from Acqui Terme (Piemonte), 2n = 30. Scale bar: 10 μm.
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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.