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1,574 results for “genome sequencing”
Analysis of Whole Genome Sequence and Genome-wide SNPs in Highly Inbred Pigs [Array]
GEO Series GSE157934. Sus scrofa. 48 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Novel MicroRNA Signature to Differentiate Ulcerative Colitis from Crohn Disease: A Genome-Wide Study Using Next Generation Sequencing
GEO Series GSE89667. Homo sapiens. 37 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Genome-wide DNA methylation analysis using next generation sequencing to reveal candidate genes responsible for boar taint in pigs
GEO Series GSE129385. Sus scrofa. 9 samples. Type: Methylation profiling by high throughput sequencing.
Whole-Genome Bisulfite Sequencing of Nasopharyngeal Carcinoma and Nasopharyngeal Epithelial Tissues
GEO Series GSE173563. Homo sapiens. 32 samples. Type: Methylation profiling by high throughput sequencing.
Identification of a RAI1-associated disease network through integration of exome sequencing, transcriptomics and 3D genomics
GEO Series GSE83420. Homo sapiens. 2 samples. Type: Other.
Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure
GEO Series GSE200047. Homo sapiens. 4 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Genome-wide binding of SEPALLATA3 (SEP3) and AGAMOUS (AG) complexes determined by sequential DNA-affinity purification sequencing
GEO Series GSE150528. Arabidopsis thaliana. 10 samples. Type: Other.
Genomic Sequencing of Pediatric Rhabdomyosarcoma
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood accounting for approximately 350 newly diagnosed cases yearly in the United States. With the development of multimodal chemotherapy regimens, relapse-free survival rates have improved to 70-80% in patients with localized disease albeit with significant toxicity. Unfortunately, despite aggressive treatment, patients with metastatic or recurrent disease continue to suffer from high mortality. Further characterization of the genetic events underlying this tumor type is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. In a collaborative effort between the National Cancer Institute, the Children's Oncology Group, and the Broad Institute, we use a combination of whole-genome and whole-exome sequencing to characterize the landscape of somatic alterations in tumor/normal pairs.
Genomic Sequencing of Ewing's Sarcoma
The Ewing sarcoma family of tumors is a group of malignant small round blue cell tumors that arise in bone or soft tissue. Ewing sarcoma (ES) is the second most common type of primary bone tumor to affect children and adolescents and accounts for 2.9% of all childhood cancers. This dataset reports whole-genome sequencing of primary Ewing's Sarcoma samples and matching germline samples.
Genomic Sequencing of Ewing Sarcoma
Pediatric Ewing sarcoma is a pediatric cancer that primarily arises from the bone. It is characterized by chimeric fusions of the EWS gene and an ETS family transcription factor. In this study, we performed massively parallel sequencing of a larger collection of Ewing sarcoma tumors to define the genomic landscape of this disease. We found that these tumors are among of the most genetically normal cancers currently characterized. There was also a marked absence of recurrent mutations in immediately targetable signaling transduction pathway genes. In this study we answer outstanding questions about ETS transcription factor expression, effects of treatment on mutational burden in Ewing sarcoma tumors, and describe patterns of tumor evolution. We also found that loss-of-function mutations in STAG2 were present in approximately 15% of Ewing sarcoma tumors and loss of STAG2 expression was associated with disease metastasis in this patient cohort.
Genome-wide DNA methylation sequencing in C2C12 myoblasts and myotubes
GEO Series GSE141047. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Whole genome bisulfite sequencing analysis to examine the effect of the iron chelator deferoxamine on DNA methylation levels in 3T3-L1 pre-adipocyte cells
GEO Series GSE174134. Mus musculus. 15 samples. Type: Methylation profiling by high throughput sequencing.
Data from: Development and validation of a core genome multilocus sequence typing (cgMLST) scheme for Klebsiella oxytoca
<p>The dataset hereby shared contains the genomes used to create and validate a newly proposed schema for <i>Klebsiella oxytoca.</i> </p><p>As reference dataset, all publicly available <i>K. oxytoca</i> draft and complete genomes (199) were downloaded from RefSeq in NCBI database in September 2021. All assemblies were filtered by quality and identification methods in order to remove highly fragmented genomes (more than 200 contigs) and genomes that did not correspond to <i>K. oxytoca sensu stricto</i>. A series of assemblies, including complete and draft genomes, were removed because they (i) did not correspond to <i>K. oxytoca</i> species based on MLST or rMLST, and because they (ii) produced ANI values lower than 96% against <i>K. oxytoca</i>. Apart from some genomes that had no correspondence to<i> K. oxytoca,</i> several others were discarded because they did not correspond to <i>K. oxytoca </i>species sensu stricto, but other closely related species included in the <i>K. oxytoca </i>species complex, such as <i>K. michiganensis</i> or <i>K. grimontii.</i> Additional identification of blaOXY gene variants supported this observation. Finally, genomes that had not been assigned an assigned ST were also removed, since they would not contribute to the schema validation. Therefore, the final dataset consisted in 16 high-quality complete genomes of <i>K. oxytoca sensu stricto. </i></p><p> </p>
Deciphering complex antibiotic resistance patterns in Helicobacter pylori through whole genome sequencing and machine learning
<p>Whole Genome Sequencing of <em>Helicobacter pylori</em> (<em>Hp</em>).</p>
Genome annotations of bacterial scaffold sequences obtained from surfaces of the International Space Station
<p>Master annotations in GFF3 format, containing both scaffold sequences and annotations, of 226 bacterial isolates obtained from the International Space Station (ISS) during Microbial Tracking-1 flight experiments. These files can be viewed directly in Artemis or IGV. The analysis was performed with Prokka 1.14.5 (<a href="https://doi.org/10.1093/bioinformatics/btu153">Seemann, 2014</a>).</p> <p>Raw sequencing data and sequence assemblies in FASTA format can be downloaded from the NASA GeneLab repository <a href="https://genelab.nasa.gov/">https://genelab.nasa.gov</a>, the first comprehensive space-related omics database.</p>
Data from: Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement
Abstract missing
Genome in a Bottle Direct-RNA Sequencing: GM24631 Calibration-Strand Aligned Reads
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Fig 3 in Whole-Genome Optical Mapping and Finished Genome Sequence of Sphingobacterium deserti sp. nov., a New Species Isolated from the Western Desert of China
Fig 3. Optical mapping of the Sphingobacterium deserti sp. nov. ZWT genomic DNA with BamHI. The large chromosome restriction map was generated by shotgun optical mapping. The outer circle depicts the consensus map; the inner circles indicate the contigs from which the consensus map was generated. Colors are arbitrarily assigned to homologous overlapping fragments. doi:10.1371/journal.pone.0122254.g003
Fig. 1 Biomphalaria glabrata genomic scaffold ASM4573v1 in ELAV Intron 8: a single-copy sequence marker for shallow to deep phylogeny in Eupulmonata Hasprunar & Huber, 1990 and Hygrophila Férussac, 1822 (Gastropoda: Mollusca)
Fig. 1 Biomphalaria glabrata genomic scaffold ASM4573v1 LG4_Random_Scaffold46, whole genome shotgun sequence, with the location of Exons 8 and 9, Intron 8, and primers used for ELAVI8 PCR amplification
Supplementary Table S2. DNA polymorphisms in gene sequences of 56 sea buckthorn accessions based on the analysis of whole-genome sequencing data.
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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.