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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RIKEN integrated database of mammals Resource Report Resource Website |
RIKEN integrated database of mammals (RRID:SCR_006890) | RIKEN integrated database of mammals | data or information resource, database, portal |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2019. A database that integrates not only RIKEN''''s original large-scale mammalian databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists'''' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. |
integration, network, standardization, biomedical, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Functional Annotation of the Mammalian Genome is related to: Cerebellar Development Transcriptome Database is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: OBO has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:21076152 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151886, biotools:riken | https://bio.tools/riken | SCR_006890 | 2026-08-29 11:28:43 | 0 | |||||
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SpliceDB Resource Report Resource Website 1+ mentions |
SpliceDB (RRID:SCR_006262) | SpliceDB | data or information resource, data set | Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs. | gene, expressed sequence tag, splice, canonical, non-canonical, splice site, sequence, data set, splice site sequence |
is listed by: OMICtools is listed by: 3DVC is related to: GenBank has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11125105 PMID:11058137 |
nlx_151853, OMICS_01892 | http://linux1.softberry.com/berry.phtml?topic=splicedb | http://genomic.sanger.ac.uk/spldb/SpliceDB.htm | SCR_006262 | SpliceDB: canonical and non-canonical splice site sequences in mammalian genes | 2026-08-29 11:32:03 | 2 | |||||
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MVZ Collections Resource Report Resource Website 1+ mentions |
MVZ Collections (RRID:SCR_010608) | MVZ Collections | biomaterial supply resource, material resource | A collection of over 640,000 specimens of amphibians, reptiles, birds, bird eggs or nests, and mammals, as well as over 50,000 tissue samples from these vertebrate groups. These research collections are ranked as one of the largest in the United States, and the largest of any university museum. In addition, the Museum has numerous special collections that include archived field notes and photographs, historical annotated maps and correspondence, avian sound recordings, chromosome and histology preparations, Milton Hildebrand anatomical and film collections, artwork related to terrestrial vertebrate natural history, and a library of books, reprints, and journals for curation and research activities. Specimen data are accessible online, and the Museum is working to improve data access to the other collections. Museum Collections * Mammal Collection * Herpetological Collection * Bird Collection * Egg & Nest Collection * Tissue Collection * Fieldnotes, Photos, & Map Collection * Other Collections The Museum of Vertebrate Zoology (MVZ) welcomes donations of amphibians, reptiles, birds, bird eggs and nests, mammals and related materials. Acceptance of a donation is at the discretion of MVZ Curators. * Specimens -- May include preserved specimens and/or parts (e.g., tissue samples) as well as unpreserved material (e.g., frozen carcasses, live animals) that will be prepared by Museum Curators, curatorial staff, or students. * Related Materials -- Donations of images (digital or printed photographs or slides), sound recordings, field notes, and other natural history archival material. Materials must be connected to specimens or research projects. Donated material and associated data will be made available for research, education, or public exhibit according to the mission and policies of the Museum and Regents, except by prior signed agreement between the donor and the Museum. | tissue, dna, egg, nest, tissue, blood, protein extract, skin, skeleton |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Museum of Vertebrate Zoology |
Will provide limited grants of tissue from its collections to qualified researchers | nlx_51505 | SCR_010608 | Museum of Vertebrate Zoology Collections | 2026-08-29 11:31:03 | 1 | |||||||
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ChEA Resource Report Resource Website 100+ mentions |
ChEA (RRID:SCR_005403) | ChEA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software application, software resource | Data analysis service for gene-list enrichment analysis against a manual database. It allows users to input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The database integrates interaction data from ChIP-chip, ChIP-seq, ChIP-PET and DamID studies and contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes. | chip, transcription factor, interaction, mrna expression, gene, target gene, command-line, chip-chip, chip-seq |
is listed by: OMICtools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:20709693 | OMICS_00526 | SCR_005403 | ChIP Enrichment Analysis | 2026-08-29 11:27:28 | 280 | |||||||
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CSHL - Hannon Lab Resource Report Resource Website 50+ mentions |
CSHL - Hannon Lab (RRID:SCR_005982) | Hannon Lab | data or information resource, laboratory portal, organization portal, portal | The Hannon laboratory comprises a broad spectrum of programs in small RNA biology, mammalian genetics and genomics. We study RNAi and related pathways in a wide variety of organisms to extract common themes that define both the mechanisms by which small RNAs act and the biological processes which they impact. Currently, we focus on microRNAs, endogenous siRNAs and piRNAs and their roles in gene regulation, cancer biology, stem cell biology and in defense of the genome against transposons. In collaboration with Steve Elledge (Harvard) and Scott Lowe (CSHL), we develop genome-wide shRNA tools for RNAi-based genetics in mammalian cells, and we are now producing similar collections of artificial microRNAs for Arabidopsis with Detlef Weigel (MPI), Dick McCombie (CSHL) and Rob Martienssen (CSHL) as part of the 2010 project (see 2010.cshl.edu). Our genomic efforts include the application of RNAi-based genetic screens to cancer biology and stem cells. We also make heavy use of next generation sequencing methodologies for probing small RNA populations, in part as a member of the ENCODE consortium (with Tom Gingeras, CSHL). Finally, we develop (with Dick McCombie) and apply focal re-sequencing methods for identifying disease relevant mutations, for probing the epigenetic landscape and for the study of human evolution. | rnai, rna, mammal, genetics, genomics, microrna, sirna, pirna, gene regulation, cancer biology, stem cell biology, defense, genome, transposon, cancer, stem cell | has parent organization: Cold Spring Harbor Laboratory | nlx_151354 | SCR_005982 | Cold Spring Harbor Laboratory - Hannon Lab | 2026-08-29 11:22:28 | 70 | ||||||||
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Brad Smith Magnetic Resonance Imaging of Embryos Resource Report Resource Website |
Brad Smith Magnetic Resonance Imaging of Embryos (RRID:SCR_006300) | Brad Smith MRI of Embryos | data or information resource, data set, image collection, video resource | Data set of image collections and movies including Magnetic Resonance Imaging of Embryos, Human Embryo Imaging, MRI of Cardiovascular Development, and Live Embryo Imaging. Individual MRI slice images, three-dimensional images, animations, stereo-pair animations, animations of organ systems, and photo-micrographs are included. | embryo, magnetic resonance imaging, embryonic development, magnetic resonance microscopy, cardiovascular development, cardiovascular, development, heart, blood vessel, in-utero, in-vitro, embryonic mouse, newborn mouse, embryonic human |
is related to: Magnetic Resonance Microscopy of Mouse Embryo Specimens is related to: Multi-Dimensional Human Embryo has parent organization: University of Michigan; Ann Arbor; USA |
Normal, Mutant, Gentically-manipulated | nlx_151971 | SCR_006300 | Brad Smith Research MRI of Embryos, Brad Smith Research | 2026-08-29 11:22:34 | 0 | |||||||
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MatrixDB Resource Report Resource Website 50+ mentions |
MatrixDB (RRID:SCR_001727) | MatrixDB | data or information resource, database, production service resource, service resource | Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions. | extracellular, protein fragment, biomolecule, cation, cleavage, collagen, glycosaminoglycan, human, interaction, laminin, lipid, mammalian, matricryptin, matrikin, matrix, molecule, monomer, mulimerization, multimer, polysaccharide, protein, protein-carbohydrate interaction, protein-protein interaction, recognition, thrombospondin, interactome, extracellular protein, protein-polysaccharide interaction, extracellular interaction, molecular interaction, model organism, inorganic, small molecule-protein, small molecule, extracellular matrix protein, protein-glycosaminoglycan interaction, bio.tools, FASEB list |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: Gene Ontology is related to: PSI-MI is related to: HPRD - Human Protein Reference Database is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: Claude Bernard University Lyon 1; Lyon; France |
European Union contract FP7-HEALTH-2007-223411 | PMID:20852260 PMID:19147664 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:matrixdb, r3d100010672, nif-0000-10226 | https://bio.tools/matrixdb, https://doi.org/10.17616/R3M03H | http://matrixdb.ibcp.fr/ | SCR_001727 | MatrixDB: Extracellular Matrix Interactions Database, Extracellular Matrix Interactions Database | 2026-08-29 11:20:49 | 95 | |||
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MouseCyc Resource Report Resource Website 10+ mentions |
MouseCyc (RRID:SCR_001791) | MouseCyc | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. | energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic |
is related to: Mouse Genome Informatics (MGI) is related to: Gene Ontology has parent organization: Jackson Laboratory |
NHGRI HG003622 | PMID:19682380 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10303 | SCR_001791 | MouseCyc database, Mouse Genome Informatics: MouseCyc database | 2026-08-29 11:21:06 | 10 | |||||
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MPO Resource Report Resource Website 10+ mentions |
MPO (RRID:SCR_004855) | MPO, MP | controlled vocabulary, data or information resource, ontology | Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome. | mus, phenotype, obo |
is used by: NIF Data Federation is listed by: BioPortal is related to: Rat Genome Database (RGD) is related to: MouseBook is related to: Neurocarta is related to: phenomeNET has parent organization: OBO has parent organization: Mouse Genome Informatics (MGI) |
PMID:17989687 | The community can contribute to this resource | nlx_83784 | http://obofoundry.org/cgi-bin/detail.cgi?id=mammalian_phenotype, http://purl.bioontology.org/ontology/MP | SCR_004855 | Mammalian Phenotype Ontology | 2026-08-29 11:22:01 | 19 | |||||
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Program on Ontologies of Neural Structures Resource Report Resource Website |
Program on Ontologies of Neural Structures (RRID:SCR_003549) | PONS | data or information resource, narrative resource, portal, standard specification, topical portal | Program consisting of three Task Forces and one Working Group to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. Closely linked to the Program on Digital Brain Atlasing, the Program aims to establish a structured lexicon for the translation and definition of terms describing neural structures at multiple levels of granularity. The three Task Forces and one Working Group involved in the PONS effort: * Structural lexicon * Neuron registry * Representation and deployment * KnowledgeSpace Working Group Structural lexicon, Neuron registry, Representation and deployment, and KnowledgeSpace Working Group. | neural structure, lexicon, neuroanatomy, brain, metadata, brain region, data sharing, neuron, interoperability |
is related to: NeuroLex is related to: Neuron Registry Curator Interface has parent organization: International Neuroinformatics Coordinating Facility |
nlx_157669 | SCR_003549 | INCF Program on Ontologies of Neural Structures | 2026-08-29 11:21:58 | 0 | ||||||||
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Common Upper Mammalian Brain Ontology Resource Report Resource Website |
Common Upper Mammalian Brain Ontology (RRID:SCR_003629) | CUMBO | controlled vocabulary, data or information resource, ontology | Ontology of formal definitions (i.e., machine processable) for the types of structures commonly described in neuroanatomy. | neuroanatomy, brain |
is related to: Linked Neuron Data has parent organization: International Neuroinformatics Coordinating Facility has parent organization: NeuroLex |
nlx_157809 | http://neurolex.org/wiki/Cumbo_terms | SCR_003629 | INCF-CUMBO, Common Upper Mammalian Brain Ontology (CUMBO) | 2026-08-29 11:21:36 | 0 | |||||||
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BioCyc Resource Report Resource Website 1000+ mentions |
BioCyc (RRID:SCR_002298) | data or information resource, database | A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site. | database, pathway/genome databases, PGDB, genome, metabolic pathway, microbiome, FASEB list |
uses: Pathway Tools is used by: PathCase Pathways Database System lists: Pathway Tools lists: EcoCyc lists: MetaCyc lists: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is listed by: LabWorm is listed by: Human Microbiome Project is related to: Pathway Tools is related to: PathCase Pathways Database System is related to: EcoCyc is related to: MetaCyc is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: EcoCyc is related to: Gramene is related to: NCBI BioSystems Database is related to: KOBAS is related to: Tuberculosis Database is related to: Pathway Tools has parent organization: Stanford Research Institute International |
NIGMS GM080746 | PMID:16246909 | Restricted | nif-0000-00369, r3d100011259 | https://doi.org/10.17616/R36G8H | SCR_002298 | BioCyc Database Collection | 2026-08-29 11:21:17 | 1063 | |||||
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Blue Brain Project Resource Report Resource Website 10+ mentions |
Blue Brain Project (RRID:SCR_002994) | Blue Brain | data or information resource, portal, topical portal | A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain. | brain, neuron, microcircuit, simulation, cortex, cortical column, model |
is related to: NeuroCurator has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland is parent organization of: ChannelPedia provides: Blue Brain Cell Atlas |
Neurological disease | nif-0000-30208 | SCR_002994 | Bluebrain | 2026-08-29 11:21:23 | 22 | |||||||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-08-29 11:22:58 | 6 | |||||
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ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-08-29 11:22:10 | 30 | ||||||
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TargetScan Resource Report Resource Website 10000+ mentions |
TargetScan (RRID:SCR_010845) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals. | predict, biological, target, miRNA, conserved, 8mer, 7mer, site, match seed, region, nonconserved, mismatched, pair |
is listed by: OMICtools is listed by: SoftCite has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Howard Hughes Medical Institute ; NIGMS GM067031; NSF Graduate Research Fellowship |
PMID:26267216 | Free, Freely available | OMICS_00420 | http://www.targetscan.org/vert_71/ | SCR_010845 | TargetScanFly | 2026-08-29 11:23:39 | 11785 | |||||
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NetOGlyc Resource Report Resource Website 500+ mentions |
NetOGlyc (RRID:SCR_009026) | NetOGlyc | analysis service resource, data analysis service, production service resource, service resource, software application, software resource | Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins. | neural network, predict, mucin, galnac, o-glycosylation site, protein, o-glycosylation, glycoprotein, o-glycoproteome, glycosite, proteome, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: CBS Prediction Servers |
PMID:23584533 | Acknowledgement requested | nlx_153864, biotools:netoglyc | https://bio.tools/netoglyc | SCR_009026 | NetOGlyc Server | 2026-08-29 11:23:17 | 643 | |||||
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UD Chick EST Project Resource Report Resource Website 10+ mentions |
UD Chick EST Project (RRID:SCR_002236) | biomaterial supply resource, cell repository, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created. | gene, avian, cdna, chicken, clone, cytokine, dna, homology, immunology, mammalian, molecular, nucleotide, poultry, receptor, sequence, splenocyte, t cell |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Delaware; Delaware; USA |
PMID:16554550 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20971 | SCR_002236 | U.D. Chick EST Database, University of Delaware Chick EST Project, University of Delaware Chick EST Database | 2026-08-29 11:28:39 | 18 | |||||||
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BioRep Resource Report Resource Website 100+ mentions |
BioRep (RRID:SCR_004907) | BioRep | biomaterial supply resource, cell repository, material resource | Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories. | chromosome analysis, dhplc analysis, methylation, genotyping, gender analysis, sequencing service, nucleic acid isolation, catalog, cell line, dna, cell, tissue, frozen, liquid nitrogen, vapor nitrogen, refrigerator, fixed, paraffin embedded, slide, cryogenic, paraffin block, cryopreserved, molecular biology, microbiology, cytogenetics, media preparation, tissue microarray, cell array, frozen array, cell biology, research, transplantation, custom, blood, tissue, ebv transformed lymphoblast culture, fibroblast cell culture, nucleic acid, sequence, mycoplasma, karyotype |
is listed by: One Mind Biospecimen Bank Listing is related to: Coriell Institute for Medical Research |
Public: offer biorepository services to public and private research institutes, To the highest standards of quality and safety. BioRep is one of the few ''''Global Biorepository'''' able to serve the pharmaceutical industries for world wide clinical trials. | nlx_87504 | http://www.biorep.it/eng/ | SCR_004907 | 2026-08-29 11:28:42 | 187 | |||||||
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ARACNE Resource Report Resource Website 100+ mentions |
ARACNE (RRID:SCR_002180) | ARACNE | software application, software resource | An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis. | cellular network, cellular, network, microarray, expression profile, deconvolution, regulatory network |
is listed by: OMICtools is related to: B Cell Interactome has parent organization: Columbia University; New York; USA |
PMID:16723010 | Free, Freely available | OMICS_01851 | SCR_002180 | Algorithm for the Reconstruction of Accurate Cellular Networks | 2026-08-29 11:30:40 | 163 |
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