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3,584
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3,584 results for “genomic analysis”
Genome-wide target analysis of Class III HD-ZIP transcription factors [ChIP-Seq]
GEO Series GSE80686. Arabidopsis thaliana. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Source-tracking fecal contamination by genomic analysis of Escherichia coli from human and animal hosts
GEO Series GSE21115. Escherichia coli str. K-12 substr. MG1655; Escherichia coli. 24 samples. Type: Genome variation profiling by array.
Pancancer Analysis of Whole Genomes
The Pancancer Analysis of Whole Genomes (PCAWG) study is an international collaboration to identify a comprehensive catelog of genomic, transcriptomic and epigenomic changes in 2,778 cancer whole genomes, across 47 tumor types from the International Cancer Genome Consortium.
Enabling Whole Genome Sequencing Analysis from FFPE Specimens in Clinical Oncology
This study includes whole genome sequencing from 44 pediatric patients at Memorial Sloan Kettering derived from formalin-fixed paraffin-embedded (FFPE) tissue. This dataset was used to train and validate a classification strategy called FFPErase for detecting artifact mutations from FFPE damage.
Gabriella Miller Kids First Pediatric Research Program: An Integrated Clinical and Genomic Analysis of Treatment Failure in Pediatric Osteosarcoma
Although the survival of children with relapsed osteosarcoma is very poor, little is known about the etiology of treatment failure in this disease. The purpose of this project is to perform whole genome sequencing on serial samples from patients with osteosarcoma obtained before treatment, after treatment, and at relapse/metastasis in order to identify the mutations and pathways that are drivers of drug resistance. If successful, our results may help identify patients at high risk for treatment failure and may yield new treatments for children who cannot currently be cured.
Genomic Analysis in Pediatric Malignancies
Pediatric solid tumors are highly heterogeneous, encompassing a large number of histotypes. The genomic landscape of these diseases is characterized by few singleucleotide variants (SNVs) compared to adult cancers. In contrast, many exhibit a high prevalence of structural or epigenetic changes that alter gene expression, underlining the need for comprehensive genomic approaches such as whole-genome sequencing (WGS). Several studies have specifically addressed the clinical utility of genomic analysis in the pediatric and AYA cancer setting. Review of these studies point to key challenges that must be addressed in order to advance the routine use of genomics in this population. We have established a large collection of solid tumor tissue samples through our biobanking efforts. Where possible, we obtain longitudinal samples from the same patient. These primary patient samples and their corresponding germline have been analyzed using whole genome and whole transcriptome sequencing methods and have been linked to clinical metadata using both manual curation and robust methods for automatic extraction from the electronic health record (EHR). Importantly, research-grade genomic analysis is performed in parallel to our CLIA-grade sequencing (“UCSF500”) efforts described in the companion P30 supplement for clinical data sharing. For our sequenced tumor samples, we have retrospective clinical data and ongoing efforts to prospectively record key events throughout the patient’s cancer journey. In our solid tumor program, we have developed many patient-derived xenograft models and a number of PDX-derived cell lines. These unique models have been evaluated using genomic and functional approaches including (in some cases) treatment with conventional chemotherapy or investigational agents. Lastly, these samples were collected from a population that is among the most diverse in the nation and includes significant numbers of Asian, Latino, Indigenous and African-American patients, groups that are traditionally underrepresented in many banking efforts.
Gabriella Miller Kids First Pediatric Research Program: An Integrated Clinical and Genomic Analysis of Treatment Failure in Pediatric Osteosarcoma
Open the record for dataset details and reuse information.
Genome-wide analysis of wild type and prmt5 mutant plants (Experiment A)
GEO Series GSE149429. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Genome-wide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor Homothorax in Drosophila
GEO Series GSE23864. Drosophila melanogaster. 5 samples. Type: Genome binding/occupancy profiling by genome tiling array.
Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement
<p>Leaf shape traits and metabolomic traits data for GWAS analysis</p>
Genome analysis and population genomics of sexual and asexual nematodes - Mater Thesis Laura Villegas
<p>Results obtained during my master thesis as well as files used to generate plots. Commands implemented to obtain the results and scripts to obtain plots with the here presente data can be found in https://github.com/lauraivillegasr/master_thesis</p>
Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi
<p>Supplementary Materials of Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi</p> <p>Supplementary Materials: The following materials are available online. <br> Table S1: General tRNA features in the four cordyceps mitogenomes.<br> Table S2: Complete mitochondrial genome characteristics for the four cordyceps analyzed here. <br> Table S3: Local BLAST analysis of the four cordyceps mitogenomes against themselves. <br> Table S4: Tandem repeats detected in the mitogenomes of cordyceps using the Tandem Repeats Finder program. <br> Table S5: Distribution of repeat loci in the four cordyceps mitogenomes identified by REPuter. </p>
Genome wide transcriptomic analysis of M82 genotype and one S. pennellii accession inoculated with the AM fungus Funneliformis mosseae under combined drought and low nutrient stress
<p>The aim of this experiment is to study transcriptome of tomato cv ‘M82’ and <em>S. pennellii </em>(LA5240) considering as factors combined nutrients and water stress, mycorrhization and the interaction between them. We grew plants under controlled conditions using <em>Funneliformis mosseae </em>as mycorrhizal fungus, a well-known symbiont for tomato. Combined water and nutrient stress was applied on 1 month old plants and maintained for 1 month, reducing up to 40% phosphorus, nitrogen and water provision. At the end of the experiment plant growth response was measured, AM colonization checked and RNA isolated from roots and sequenced. Data analysis is still in progress and only results produced until now are here provided (April-December 2018).</p>
Datasets of "Lipoxygenase (LOX) genes in angiosperms: a comparative genome-wide analysis"
<p>This dataset represent FASTA files containing coding sequences (CDS) and protein sequences used for all phylogenetic analyses of the study " Lipoxygenase (LOX) genes in angiosperms: a comparative genome-wide analysis" (submitted).</p>
Genome-wide analysis of replication timing in ESC and 2CLC [stable]
GEO Series GSE136226. Mus musculus. 12 samples. Type: Other.
3D genomics analysis identifies enhancer hijacking caused by structural alterations and extrachromosomal circular DNA formation [RNA-Seq]
GEO Series GSE247056. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis
GEO Series GSE93286. Homo sapiens. 6 samples. Type: SNP genotyping by SNP array.
Genome-wide analysis of MCF-7 cells expressing or not MMP-14 (MT1-MMP) growing in monolayer cell culture conditions
GEO Series GSE64320. Homo sapiens. 2 samples. Type: Expression profiling by array.
Analysis of copy number change in cord lining epithelial cells after phage integrase mediated genomic integration.
GEO Series GSE12629. Homo sapiens. 4 samples. Type: Genome variation profiling by SNP array.
High resolution analysis of early lobular neoplastic breast lesions (ALH and LCIS) by whole genome tiling path array CGH
GEO Series GSE4591. Homo sapiens. 25 samples. Type: Genome variation profiling by genome tiling array.
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.