Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
70
datasets available to search
ShareScore release 0.9.0
Dataset results
70 results for “Genome doubling”
Single-cell mouse and PC9 data for "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability"
<p>This repository includes the processed data (including copy number profiles and related analysis) for the E/EP mouse tumors and for the PC9 resistance cell lines for all the analyses of the manuscript "TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response through Chromosomal Instability".</p><p>The code for the related analyses is available in GitHub at https://github.com/zaccaria-lab/TP53loss_WGD</p>
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 in The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing
Figure 2. – Maximum Likelihood phylogenetic tree inferred with the 13 protein coding genes. The values of bootstrap are represent- ed beside the nodes.
Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)
<p>Initial filtered ddRADseq dataset with highly variable SNP markers from native American and Hungarian <em>Robinia pseudoacacia</em> L. individuals</p>
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses
Our knowledge of the diversity and frequency of genomic structural variation segregating in populations of large double stranded (ds) DNA viruses is limited. Here we sequenced the genome of a baculovirus (AcMNPV) purified from beet armyworm (Spodoptera exigua) larvae at depths >195,000X using both short-read (Illumina) and long-read (PacBio) technologies. Using a pipeline relying on hierarchical clustering of structural variants (SVs) detected in individual short- and long-reads by six variant callers, we identified a total of 1,141 SVs in AcMNPV, including 464 deletions, 443 inversions, 160 duplications and 74 insertions. These variants are considered robust and unlikely to result from technical artifacts because they were independently detected in at least three long reads as well as at least three short reads. SVs are distributed along the entire AcMNPV genome and may involve large genomic regions (30,496 bp on average). We show that no less than 39.9% of genomes carry at least one SV in AcMNPV populations, that the vast majority of SVs (75%) segregate at very low frequency (<0.01%) and that very few SVs persist after 10 replication cycles, consistent with a negative impact of most SVs on AcMNPV fitness. Using short-read sequencing datasets, we then show that populations of two iridoviruses and one herpesvirus are also full of SVs, as they contain between 426 and 1102 SVs carried by 52.4 to 80.1% of genomes. Finally, AcMNPV long reads allowed us to identify 1,757 transposable elements (TEs) insertions, 895 of which are truncated and occur at one extremity of the reads. This further supports the role of baculoviruses as possible vectors of horizontal transfer of TEs. Altogether, we found that SVs, which evolve mostly under rapid dynamics of gain and loss in viral populations, represent an important feature in the biology of large dsDNA viruses.
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>
All-atom models of SU10 and P68 viral genomes. Supplementary to the "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses".
<p>The dataset contains mmCIF formatted all-atom models of SU10 and P68 viral genomes and the python script used for refinement of the initial MMB-generated coordinates.</p>
Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double stranded DNA viruses
Open the record for dataset details and reuse information.
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C peaks represent diploid cells, and 4C peaks represent cells in the G2 phase of the cell cycle, with replicated DNA. Standard used: Solanum pseudocapsicum 2C = 2.61 pg. A, Himacerus apterus female with 2n = 36 + XX and 2C = 9.71 pg. B, Nabis maoricus female with 2n = 16 + XX and 2C = 4.21 pg.
Figure 2 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 2. Nuclear DNA content stained with propidium iodide (PI) compared with relative nuclear DNA content stained with 4′,6-diamidino-2-phenylindole (DAPI). The line represents the trend in GC content, with a minimum of 33.34% and a maximum of 37.83%. Each pair of black and white symbols represents one specimen, as follows: circles, females; squares, males; white symbols, DAPI; black symbols, PI.
Figure 1 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 1. Chromosomes of Nabidae species studied, stained with Giemsa (A, D, F, G, M) or with an 18S ribosomal DNA (rDNA) probe (red) applied via fluorescence in situ hybrization (FISH) (B, C, E, H–L, N–P). A, B, Nabis punctatus ♀ 2n = 16 + XX, mitotic metaphase. C, Himacerus apterus ♀ 2n = 36 + XX, mitotic metaphase. D, Nabis rugosus ♂ 2n = 16 + XY + 1 metaphase I, specimen with an additional chromosome (arrow). E, Nabis maoricus ♀ 2n = 18 + XX, mitotic metaphase. F, N. maoricus ♂ 2n = 16 + XY, postpachytene, with sex chromosomes superspiralized. G, H, Nabis biformis ♀ 2n = 16 + XX, mitotic metaphase, with two 18S rDNA signals on each X chromosome. I, Nabis limbatus ♀ 2n = 16 + XX, mitotic metaphase, species with the most distal 18S rDNA signal. J, N. rugosus ♂ 2n = 16 + XY, mitotic metaphase, species with the two 18S rDNA signals on Y chromosome. K, Prostemma guttula ♂ 2n = 26 + XY, metaphase II. L, N. maoricus ♂ 2n = 16 + XY, metaphase II, with Y chromosome showing no 18S rDNA signal. M, N, Prostemma aeneicolle ♀ 2n = 26 + XX, mitotic metaphase. O, H. apterus ♀ 2n = 36 + XXXX, mitotic metaphase, with terminal 18S rDNA signals on four X chromosomes originated by fragmentation. P, N. maoricus ♀ 2n = 18 + XXX, mitotic metaphase, with one X chromosome fragmented outside of the 18S rDNA position. Arrowheads indicate 18S rDNA signal; X and Y are the sex chromosomes. Scale bars: 10 μm.
Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.
Figure 4 in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 4. Comparison of three alternative hypotheses on the ancestral 2n number of chromosomes of Nabidae: fusions, proposed by Nokkala et al. (2007); autosomal polyploidy, suggested by Kuznetsova & Maryańska-Nadachowska (2000) and supported by nuclear DNA content data from the present study; and the hypothetical fission theory. Abbreviations: 2C, nuclear DNA content; F, autosomal fusions; Fis, fissions; P, polyploidy.
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C in Peaceful revolution in genome size: polyploidy in the Nabidae (Heteroptera); autosomes and nuclear DNA content doubling
Figure 3. Example relative fluorescence histograms for samples stained with propidium iodide. The 2C peaks represent diploid cells, and 4C peaks represent cells in the G2 phase of the cell cycle, with replicated DNA. Standard used: Solanum pseudocapsicum 2C = 2.61 pg. A, Himacerus apterus female with 2n = 36 + XX and 2C = 9.71 pg. B, Nabis maoricus female with 2n = 16 + XX and 2C = 4.21 pg.
Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation
Open the record for dataset details and reuse information.
Figure 1. – Sequence lengths for 7760 in The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing
Figure 1. – Sequence lengths for 7760 nucleotide sequences allowing the assembling of the Thymallus thymallus mitogenome.
Whole genome doubling drives oncogenic loss of chromatin segregation [WGS]
GEO Series GSE222385. Homo sapiens. 25 samples. Type: Other.
Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo
GEO Series GSE71249. Escherichia coli. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide mapping of meiotic double-strand breaks by sequencing Spo11 oligos.
GEO Series GSE26449. Saccharomyces cerevisiae. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli
GEO Series GSE117541. Escherichia coli. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration [Mate-Pair]
GEO Series GSE227444. Mus musculus. 11 samples. Type: Other.
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.