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on page 1 showing 20 out of 350 results from 1 sources

Cite this (5 prime end Serial Analysis of Gene Expression Database, RRID:SCR_001680)

URL: http://5sage.gi.k.u-tokyo.ac.jp/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available.

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Cite this (Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus, RRID:SCR_003731)

URL: http://www.nih.gov/science/amp/autoimmune.htm

Resource Type: Resource, organization portal, portal, consortium, data or information resource

The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.

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Cite this (Adult Mouse Anatomy Ontology, RRID:SCR_006568)

URL: http://www.informatics.jax.org/searches/AMA_form.shtml

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

Ontology that organizes anatomical structures for the adult mouse (Theiler stage 28) spatially and functionally, using ''is a'' and ''part of'' relationships. The ontology is used to describe expression data for the adult mouse and phenotype data pertinent to anatomy in standardized ways. The browser can be used to view anatomical terms and their relationships in a hierarchical display.

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Cite this (AffyExpress, RRID:SCR_001321)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

Resource Type: Resource, software resource

Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

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Cite this (AffyRNADegradation, RRID:SCR_000118)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyRNADegradation.html

Resource Type: Resource, software resource

Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

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    aGEM

Cite this (aGEM, RRID:SCR_013349)

URL: http://agem.cnb.csic.es/VisualOmics/aGEM/

Resource Type: Resource, data or information resource, database

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display.

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Cite this (Allen Brain Atlas API, RRID:SCR_005984)

URL: http://www.brain-map.org/api/index.html

Resource Type: Resource, software resource, software application, source code

API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service

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Cite this (Allen Developing Mouse Brain Atlas, RRID:SCR_002990)

URL: http://developingmouse.brain-map.org/

Resource Type: Resource, atlas, database, expression atlas, reference atlas, data or information resource

A map of gene expression in the developing mouse brain revealing gene expression patterns from embryonic through postnatal stages as well as provides information about both spatial and temporal regulation of gene expression - now offering over 1,000 genes and new anatomic reference atlases. The Allen Developing Mouse Brain Atlas provides a characterization of gene expression in the brain beginning with mid-gestation through to juvenile/young adult. Building upon the foundation established by the original Allen Mouse Brain Atlas, the Allen Developing Mouse Brain Atlas provides a framework to explore temporal and spatial regulation of gene expression, effectively a 4D atlas, with a highly accessible and easily navigable free online database. When complete, this Atlas will extend the Allen Mouse Brain Atlas by offering gene expression data across seven new developmental stages. An application has been created to enable viewing of this data set, complete with tools for search and navigation of the data. As of the April 2009 release, 1,000 unique genes are available covering seven stages of the developmental process. Feature highlights in this release include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases, currently available through Level 05, may be viewed alongside the in situ hybridization (ISH) data as well as by itself. Additional in situ hybridization data, further reference atlas detail and additional search and navigation tools will be provided in future releases.

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Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

A multi-modal atlas of the human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists across a wide range of specialties. Data modalities incorporated into this resource include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download. After installing Brain Explorer 2, you can view gene expression data by performing a gene search from the Microarray page or from within Brain Explorer 2''s main window.

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Cite this (Allen Institute for Brain Science, RRID:SCR_006491)

URL: http://www.brain-map.org

Resource Type: Resource, atlas, topical portal, portal, data or information resource

Independent 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works. Utilizing the mouse model system, a multidisciplinary group of neuroscientists, molecular biologists, informaticists, engineers, mathematicians, statisticians, and computational biologists have joined together to investigate expression of 20,000 genes in the adult mouse brain and to map gene expression to a cellular level beyond neuroanatomic boundaries. The data generated from this joint effort is contained in the publicly available Allen Brain Atlas application. Molecular approaches to understanding the functional organization of the brain promise new insights into the relationships between genes, brain, behavior and disease. To facilitate such insights, the Allen Institute produces large-scale projects and makes the resulting data and tools freely available online to scientists worldwide. These open resources, all available at www.brain-map.org, are intended to foster scientific discovery and collaboration. Atlases: Allen Developing Mouse Brain Atlas: A map of gene expression in the developing mouse brain. Building on the Allen Mouse Brain Atlas, this atlas reveals gene expression patterns from embryonic through postnatal stages to provide information about both spatial and temporal regulation of gene expression. Allen Spinal Cord Atlas: A genome-wide map of gene expression throughout the adult and juvenile mouse spinal cord. The Atlas was made possible through the generous support of a diverse consortium of funders, representing disease organizations, foundations, and corporate and private donors. Allen Mouse Brain Atlas (formerly Allen Brain Atlas): A genome-wide, three-dimensional map of gene expression in the adult mouse brain. Similar in scale to the Human Genome Project, the Atlas reveals the expression patterns of approximately 20,000 genes throughout the entire adult mouse brain down to the cellular level. The Allen Institutes inaugural project, the Atlas was completed in 2006. Studies: Mouse Diversity Study: Characterization of gene expression in the brain across genetic backgrounds and sex. Expanding on the Allen Mouse Brain Atlas, this resource includes data for 49 pharmaceutical drug target genes and a selected set of additional genes across seven mouse strains and in female mice. Transgenic Mouse Study: Comprehensive characterization of the expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Human Cortex Study: A collection of gene expression data in the adult human neocortex. Providing data for several categories of genes across different cortical regions and human individuals, including control and schizophrenic cases, the dataset has the potential to enable exploration of variability in cortical gene expression across different ages, between genders across different regions of the cortex and in schizophrenia. Sleep Study: A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. The sleep study was funded by an award from the U.S. Department of Defense.

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Cite this (Allen Institute for Brain Science Sleep Study, RRID:SCR_002983)

URL: http://sleep.alleninstitute.org

Resource Type: Resource, data set, atlas, data or information resource

A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. A high-throughput colorimetric in situ hybridization platform has been used to generate cellular resolution expression data for over 200 genes. In addition, microarray data for seven brain regions from the same five experimental conditions are downloadable from the web site; and difference grids are available for viewing differences between conditions in 3-D using Brain Explorer. Sleep deprivation leads to a repertoire of cognitive, attentional and emotional deficits that are seriously detrimental in occupations requiring alertness. These deficits may be associated with changes in gene expression in specific regions of the brain. The Allen Institute is in the process of generating a collection of cellular resolution data for gene expression in the mouse brain in response to sleep deprivation and sleep state. Using the Allen Institute high throughput in situ hybridization platform, gene expression has been examined under five experimental conditions in mice in collaboration with SRI International, and the images are presented online as a resource for sleep researchers. Sleep conditions include: Sleep-deprived for 6 hours; Time of day control for sleep-deprivation; Recovery sleep (4 hours) following 6 hours of sleep deprivation; Time of day control for recovery sleep; and waking. Project data is available in the following formats: Colorimetric ISH and Nissl images for 224 genes across 5 conditions, some with replicates Microarray data for 7 brain regions across 5 conditions Difference grids for viewing differences between conditions in 3-D using Brain Explorer Microarray data is available for seven brain regions collected from five experimental conditions: sleep deprivation, recovery sleep, and three time-of-day controls. The brain regions include four regions associated with sleep-wake regulation or circadian rhythm: suprachiasmatic nucleus, locus coeruleus, tuberomammillary nucleus and lateral hypothalamus in the vicinity of the hypocretin neurons. In order to assess the effect of sleep deprivation on gene expression in regions potentially involved in mood, memory, or executive function, an additional three brain regions were analyzed by microarray: orbital cortex, cortical amygdala (posteromedial), and dorsal entorhinal cortex. 140 microarray files are available for download in text, Codelink, and Rosetta Resolver file formats. Difference Grids allow the user to navigate changes in gene expression for a given gene across two experimental conditions, such as sleep deprivation compared to its time of day control. Difference grids are available for genes which have been assayed in replicate by ISH.

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Cite this (Allen Institute for Brain Science Transgenic Mouse Study, RRID:SCR_002999)

URL: http://transgenicmouse.alleninstitute.org/

Resource Type: Resource, data set, atlas, data or information resource

A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridization (DFISH), native fluorescence of XFP (generic term for fluorescent proteins of different colors), and immunohistochemical (IHC) labeling of marker genes.

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Cite this (Allen Institute Mouse Diversity Study, RRID:SCR_008009)

URL: http://mousediversity.alleninstitute.org/

Resource Type: Resource, atlas, expression atlas, data or information resource, database

A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex.

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Cite this (Allen Mouse Brain Atlas, RRID:SCR_002978)

URL: http://mouse.brain-map.org/

Resource Type: Resource, atlas, database, data or information resource

A genome-wide, three-dimensional map of gene expression in the adult mouse brain. Similar in scale to the Human Genome Project, the Atlas reveals the expression patterns of approximately 20,000 genes throughout the entire adult mouse brain down to the cellular level. The Allen Institute's inaugural project, the Atlas was completed in 2006. The Allen Brain Atlas of the mouse brain is an interactive, genome-wide image database of gene expression with ISH and Nissl images. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level.

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Cite this (Allen Mouse Spinal Cord Atlas, RRID:SCR_007418)

URL: http://mousespinal.brain-map.org/

Resource Type: Resource, atlas, data or information resource, database

A complete genome-wide map of gene expression throughout the adult and juvenile mouse spinal cord. The Atlas provides a baseline map of the normal mouse when used to compare gene expression in diseased or injury models. The Allen Spinal Cord Atlas is an interactive database of gene expression mapped across all anatomic segments of the mouse spinal cord at postnatal days 4 and 56. The indexed set of images for the entire genome is based on RNA in situ hybridization data, and is searchable and sortable by gene, age, expression, and in the case of the adult, by the cervical, thoracic, lumbar, sacral, and coccygeal segments. Over 80 structures in the cords can be identified with the associated high-resolution Allen Spinal Cord Reference Atlas. This resource represents an unprecedented platform for exploring the spinal cord at the cellular and molecular levels. First unveiled in July 2008, the database now has 17,000 genes in both the adult and juvenile. Reference atlases for both juvenile and adult mouse spinal cords are also available. Detailed technical documents and lists of funder''s and scientific contributors to this project can be found under the Mouse Spinal Cord project tab.

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Cite this (Allen Reference Atlas, RRID:SCR_013286)

URL: http://mouse.brain-map.org/static/atlas

Resource Type: Resource, atlas, reference atlas, data or information resource

A full-color, high-resolution, Web-based digital brain atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. The Allen Mouse Brain Atlas and Reference Atlases'' data are obtained, using identical methodology, from 8-week old C57Bl/6J male mouse brain(s) prepared as unfixed, fresh-frozen tissue. The Allen Mouse Brain Reference Atlas was designed to: 1. Allow users to directly compare gene expression patterns to neuroanatomical structures in the Web application 2. Serve as a template for the development of 3D computer graphic models of the mouse brain, providing a foundation for the development of informatics based annotation tools 3. Provide a standard neuroanatomical ontology for determining structural annotation and aid in the construction of a detailed searchable gene expression database. * Coronal Atlas: 132 coronal sections evenly spaced at 100 micrometer intervals and annotated to a detail of numerous brain structures * Sagittal Atlas: 21 representative sagittal sections spaced at 200 micrometer, annotated for 71 major brain regions identified at the top level(s) of the brain structure hierarchical tree * Coronal Legend: Search for a specific structure or browse the coronal reference atlas * Sagittal Legend: Search for a specific structure or browse the sagittal reference atlas The Allen Reference Atlas can also be found in the BioPortal, http://bioportal.bioontology.org/ontologies/40133?p=terms

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Cite this (Alternative Splicing Database, RRID:SCR_007555)

URL: http://www.eurasnet.info/tools/asdatabases

Resource Type: Resource, data or information resource, database

It has been established with the intention of assembling in a central, publicly accessible site information about alternatively spliced genes, their products and expression patterns. Version 2.1 of ASDB consists of two divisions, ASDB(proteins) , which contains amino acid sequences, and ASDB(nucleotides) with genomic sequences.
SWISS-PROT uses two formats for description of alternative splicing Thus the protein sequences were selected from SWISS-PROT using full text search for both the words alternative splicing (usually in the CC lines) and varsplic (in the FT lines). In order to group proteins that could arise by alternative splicing of the same gene, we developed the clustering procedure. Two proteins were linked if they had a common fragment of at least 20 amino acids, and clusters were initially defined as maximum connected groups of linked proteins. It turned out that some clusters were chimeric, in the sense that they contained members of multi-gene families, but not alternatively spliced variants of one gene. Therefore the multiple alignments were subject to additional analysis aimed at detection of chimeric clusters.
Each cluster is represented by multiple alignment of its members constructed using CLUSTALW. The distribution of cluster size, representation of species and other relevant statistics of ASDB(proteins) can be accessed through the links below.
This processing covers the cases when alternatively spliced variants are described in separate SWISS-PROT entries. The other kinds of ASDB records, originating from the SWISS-PROT entries with the varsplic field in the feature table, usually describe the proteins that are not part of any cluster. In these cases, the information on the variable fragments of the several proteins which result from the alternative splicing of a single gene is contained in the entry itself. ASDB(proteins) entries are marked with different symbols to allow for easy differentiation among the three types: those proteins which are part of the ASDB clusters and the corresponding multialignments, those which have the information on different variants in the associated SWISS-PROT entries, and those for which the information on the variants is not available at the present time. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SWISS-PROT entries.
The ASDB(nucleotides) division was generated by collecting all GenBank entries containing the words alternative splicing and further selection of those entries that contain complete gene sequences (all CDS fields are complete, i.e. they do not have continuation signs).
Sponsors: This work was supported by the Director, Office of Energy Research, Office of Biological and Environmental Research, of the US Department of Energy under Contract No. DE-ACO3-76SF00098. Additional support came from grants from the Russian Fund of Basic Research (99-04-48347), the Russian State Scientific Program Human Genome (65/99), and the Merck Genome Research Institute (244).

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Cite this (AmaZonia: Explore the Jungle of Microarrays Results, RRID:SCR_008405)

URL: http://amazonia.montp.inserm.fr/

Resource Type: Resource, data or information resource, database

A web interface and associated tools for easy query of public human transcriptome data by keyword, through thematic pages with list annotations. Amazonia provides a thematic entry to public transcriptomes: users may for instance query a gene on a Stem Cells page, where they will see the expression of their favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6331 samples currently present in the database. Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia database, they indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications.

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Cite this (Arabidopsis thaliana Protein Interactome Database, RRID:SCR_001896)

URL: http://www.megabionet.org/atpid/webfile/

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

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Cite this (ARK-Genomics: Centre for Functional Genomics, RRID:SCR_002214)

URL: http://www.ark-genomics.org/

Resource Type: Resource, organization portal, database, core facility, service resource, portal, access service resource, data or information resource

A high-throughput technology laboratory focused on studies of genome structure and genetic variation, gene expression and gene function, it provides an extensive range of services including: * DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing * Gene expression analysis using both microarrays and Next Generation Sequencing * High throughput genotyping of SNP and copy number variants * Data collection and analysis supported in-house high performance computing facilities and expertise * Extensive EST clone collections for a number of animal species * All of the commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen * Parentage testing using microsatellites and smaller SNP panels ARK-Genomics has developed a network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to the analysis of the data often in conjunction with commercial partners. An important part of the ARK-Genomics service is the opportunity to engage with other scientists and to raise awareness through their training courses, networking events such as their successful conference series.

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