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Found 57 result(s)

ChIP-Seq Transcription Factor Data

ChIP-Seq

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We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.

Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data

Physical Mapping Data Access

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FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).

cisRED

Databases of genome-wide regulatory module and element predictions

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

TB Database

Tuberculosis Database

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<<<!!!<<< The repository is no longer available. 2018-08-29: no more access to TB Database >>>!!!<<<

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

European Variation Archive

EVA

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The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

Phenylalanine Hydroxylase Locus Knowledgebase

PAHdb

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Leiden Open Variation Database

LOVD

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LOVD portal provides LOVD software and access to a list of worldwide LOVD applications through Locus Specific Database list and List of Public LOVD installations. The LOVD installations that have indicated to be included in the global LOVD listing are included in the overall LOVD querying service, which is based on an API.

Open Tree of Life

Tree of Life - Evolution

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The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in. Early release of the tree and tools will motivate data sharing and facilitate ongoing synthesis of knowledge.

SWATHAtlas

SWATH Atlas

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SWATHAtlas is a repository of mass spectrometry data of the human proteome. The repository provides open access to libraries of SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) datasets. SWATH-MS is a method which combines both data-independent acquisition (DIA) and targeted data analysis techniques for the collection and storage of fragmentation spectra of peptides. Compared to techniques of selected reaction monitoring (SRM), SWATH-MS allows for a more extensive throughput of proteins in a sample to be targeted. The spectra collected in SWATHAtlas can be interpreted with the help of software such as OpenSWATH or Peakview.

ORegAnno

Open regulatory annotation database

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<<<!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.

Dementias Platform UK Data Portal

DPUK Data Portal

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The DPUK Data Portal brings together records of over 2 million people in a free-to-access resource. Researchers can identify which cohorts are relevant to them, apply for access to the data and then analyse it in a secure, remote environment with a complete data linkage and analysis package.

Hardwood Genomics Project

HWG

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This database serves forest tree scientists by providing online access to hardwood tree genomic and genetic data, including assembled reference genomes, transcriptomes, and genetic mapping information. The web site also provides access to tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse for browsing genomes, Apollo for community annotation and Expression Analysis to build gene expression heatmaps.

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)

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<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) >>>!!!>>> Mapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.

Screening Unit Berlin-Buch

Screening Unit Jens Peter von Kries

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The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC. See also: https://www.mdc-berlin.de/screening-unit

SilkDB 3.0

Silkworm Genome Database

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SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics

NCBI HomoloGene

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The HomoloGene database provides a system for the automated detection of homologs among annotated genes of genomes across multiple species. These homologs are fully documented and organized by homology group. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences.

SilkPathDB

Silkworm Pathogen Database

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Silkworm Pathogen Database (SilkPathDB) is a comprehensive resource for studying on pathogens of silkworm, including microsporidia, fungi, bacteria and virus. SilkPathDB provides access to not only genomic data including functional annotation of genes and gene products, but also extensive biological information for gene expression data and corresponding researches. SilkPathDB will be help with researches on pathogens of silkworm as well as other Lepidoptera insects.

MG-RAST

Metagenomics analysis server

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The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.

Canadian Epigenetics, Environment and Health Research Consortium Network

CEEHRC Network

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CEEHRC represents a multi-stage funding commitment by the Canadian Institutes of Health Research (CIHR) and multiple Canadian and international partners. The overall aim is to position Canada at the forefront of international efforts to translate new discoveries in the field of epigenetics into improved human health. The two sites will focus on sequencing human reference epigenomes and developing new technologies and protocols; they will also serve as platforms for other CEEHRC funding initiatives, such as catalyst and team grants. The complementary reference epigenome mapping efforts of the two sites will focus on a range of common human diseases. The Vancouver group will focus on the role of epigenetics in the development of cancer, including lymphoma and cancers of the ovary, colon, breast, and thyroid. The Montreal team will focus on autoimmune / inflammatory, cardio-metabolic, and neuropsychiatric diseases, using studies of identical twins as well as animal models of human disease.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

PiroplasmaDB

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A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

Mouse Models of Human Cancer database

MMHCdb

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The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer by providing electronic access to: Information on endogenous spontaneous and induced tumors in mice, including tumor frequency & latency data, Information on genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice) in which tumors arise, Information on genetic factors associated with tumor susceptibility in mice and somatic genetic-mutations observed in the tumors, Tumor pathology reports and images, References, supporting MTB data and Links to other online resources for cancer.

Candida Genome Database

CGD

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Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database. The Candida Genome Database (CGD) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans and related species. C. albicans is the best studied of the human fungal pathogens. It is a common commensal organism of healthy individuals, but can cause debilitating mucosal infections and life-threatening systemic infections, especially in immunocompromised patients. C. albicans also serves as a model organism for the study of other fungal pathogens.