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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PHAST Resource Report Resource Website 50+ mentions |
PHAST (RRID:SCR_003204) | PHAST | software resource | A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code. | evolutionary genomic, evolution, genomics, sequence alignment, phylogenetic tree, genomic annotation, functional element, protein-coding exon, conserved sequence, phylogenetic modeling, ancestral sequence, c |
is listed by: OMICtools is listed by: Debian has parent organization: Cornell University; New York; USA |
NIH ; David and Lucile Packard Foundation ; NHGRI ; University of California Biotechnology Research and Education Program ; NSF DBI-0644111; NIGMS R01-GM082901-01 |
PMID:21278375 DOI:10.1093/bib/bbq072 |
Free, Available for download, Freely available | OMICS_01557 | https://sources.debian.org/src/phast/ | SCR_003204 | Phylogenetic Analysis with Space/Time Models | 2026-08-01 12:02:28 | 58 | ||||
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Adaptive Poisson-Boltzmann Solver Resource Report Resource Website 50+ mentions |
Adaptive Poisson-Boltzmann Solver (RRID:SCR_008387) | APBS | software resource | APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. | software package, modeling, biomolecular, electrostatic, molecular, dynamics, binding energy, equilibrium, protein, ligand, solvation, kinetics, simulation, finite element |
is listed by: 3DVC is related to: Finite Element Toolkit has parent organization: Washington University in St. Louis; Missouri; USA |
IBM/American Chemical Society ; NPACI/San Diego Supercomputer Center ; W. M. Keck Foundation ; National Biomedical Computation Resource ; NSF ; NIH |
nif-0000-30035 | SCR_008387 | 2026-08-01 12:03:30 | 50 | ||||||||
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Neurogrid Resource Report Resource Website 10+ mentions |
Neurogrid (RRID:SCR_005024) | Neurogrid | instrument resource | A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices. | simulation, neuron, cortex, synapse, analog vlsi, instrument, equipment, hardware | has parent organization: Stanford University; Stanford; California | NSF ; NIH |
PMID:17959490 | nlx_97879 | SCR_005024 | 2026-08-01 12:02:52 | 14 | |||||||
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Consed Resource Report Resource Website 500+ mentions |
Consed (RRID:SCR_005650) | Consed | software resource | A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) | next-generation sequencing, graphical editor, linux, macosx, solaris, c++ |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
NIH ; NHGRI R01HG005710 |
PMID:23995391 PMID:9521923 |
Free for academic use, Free for non-profit use, Commercial license | OMICS_00879 | SCR_005650 | 2026-08-01 12:02:56 | 595 | ||||||
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NA-MIC Kit Resource Report Resource Website |
NA-MIC Kit (RRID:SCR_005616) | NA-MIC Kit | software resource | A free open source software platform consisting of the 3D Slicer application software, a number of tools and toolkits such as VTK and ITK, and a software engineering methodology that enables multiplatform implementations. It also draws on other best practices from the community to support automatic testing for quality assurance. The NA-MIC kit uses a modular approach, where the individual components can be used by themselves or together. The NA-MIC kit is fully-compatible with local installation (behind institutional firewalls) and installation as an internet service. Significant effort has been invested to ensure compatibility with standard file formats and interoperability with a large number of external applications. Users of the NAMIC Kit will typically use a combination of its many modular components. * 3D Slicer is a general purpose application. Biomedical researchers will typically use this software tool to load, view, analyze, process and save image data. Slicer has been implemented to interoperate with many other tools, including XNAT, which is an open source image database. * Slicer modules, which are dynamically loaded by Slicer at run-time, can be used to extend Slicer''''s core functionality including defining graphical user interfaces. Modules are typically used by algorithms and application developers. * Application and algorithms developers may also use NA-MIC Kit toolkits and libraries. For example, the Insight Segmentation and Registration Toolkit ITK can be used to develop slicer modules for medical image analysis. The Visualization Toolkit can be used to process, visualize and graphically interact with data. KWWidgets is a 2D graphical user interface toolset that can be used to build applications. Teem is a library of general purpose command-line tools that are useful for processing data. Finally, those individuals wishing to create and manage complex software, the NAMIC-Kit software process is available as embodied in CMake, CTest, CPack, DART and the various documentation, bug tracking and communication tools. | platform, image analysis, visualization, segmentation, registration |
is related to: 3D Slicer is related to: Insight Segmentation and Registration Toolkit is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: National Alliance for Medical Image Computing |
NIH | BSD-style license | nlx_146255 | SCR_005616 | NA-MIC-Kit | 2026-08-01 12:03:00 | 0 | ||||||
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Pennington Biomedical Research Center Resource Report Resource Website |
Pennington Biomedical Research Center (RRID:SCR_002946) | PBRC | institution | Research institute which investigates chronic disease and its triggers. | chronic disease, chronic disease research, chronic disease institute |
is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Animal Models and Phenotyping Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Molecular Mechanisms Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center Human Phenotyping Core is parent organization of: Pennington Biomedical Research Center Nutrition and Obesity Research Center is parent organization of: Louisiana State University Pennington Biomedical Nutrition Obesity Research Center Core Facility |
State of Louisiana ; U.S. Department of Agriculture ; U.S. Department of Defense ; private sector organizations and companies ; NIH |
ISNI: 0000 0001 2159 6024, grid.250514.7, Wikidata: Q7163465, nif-0000-30066 | https://ror.org/040cnym54 | SCR_002946 | Pennington Center | 2026-08-01 12:01:58 | 0 | ||||||
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ConceptMapper Resource Report Resource Website 10+ mentions |
ConceptMapper (RRID:SCR_006548) | Concept Mapper | software resource | Software tool that stores definitions of views of data, along with the ontology concepts they represent. This is a part of the Neuroscience Information Framework (NIF) code stack. | resource:google refine | has parent organization: Neuroscience Information Framework | NIH | nlx_157720 | SCR_006548 | 2026-08-01 12:03:12 | 11 | ||||||||
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Bio-Synthesis Resource Report Resource Website 100+ mentions |
Bio-Synthesis (RRID:SCR_000820) | biomaterial supply resource, material resource | A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry. | antibody, synthetic molecule, peptides, oligonucleotide, bioconjugation, protein | is listed by: ScienceExchange | NIH 263-00050713-01 | nlx_152297, SciEx_516 | SCR_000820 | Bio-Synthesis Inc. | 2026-08-01 12:10:32 | 167 | ||||||||
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Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) Resource Report Resource Website |
Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) (RRID:SCR_004327) | RD-HUB | biomaterial supply resource, material resource | A database of biospecimens collected, stored, and distributed by biorepositories in the United States and around the globe. Its goals are: To help and assist interested parties and investigators search, locate, and identify desired biospecimens needed for their research; to facilitate collaboration and sharing of material and data among investigators across the globe; to accelerate research to facilitate the discovery of new treatments, therapeutics and eventually cures for rare diseases as well as common diseases; to identify, locate and increase the awareness of existing biorepositories across the globe; and to link the RD-HUB with the Global Rare Diseases Patient Registry and Data Repository (GRDR). | rare disease, disease, public |
lists: NIDDK Central Repository lists: National Disease Research Interchange is listed by: NIH Data Sharing Repositories is listed by: One Mind Biospecimen Bank Listing is listed by: Accelerated Cure Project MS Repository is listed by: Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center is listed by: NIDDK Information Network (dkNET) is related to: GRDR has parent organization: Office of Rare Diseases Research |
Rare disease, Aging | NIH | PMID:20609392 | Public, The community can contribute to this resource | nlx_143682 | http://biospecimens.ordr.info.nih.gov/ | SCR_004327 | Biospecimens / Biorepositories: Rare Disease-HUB, Biospecimens/Biorepositories: Rare Disease-HUB, Rare Disease-HUB | 2026-08-01 12:10:36 | 0 | |||
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KI Biobank - TwinGene Resource Report Resource Website 10+ mentions |
KI Biobank - TwinGene (RRID:SCR_006006) | TwinGene | biomaterial supply resource, material resource | In collaboration with GenomeEUtwin, the TwinGene project investigates the importance of quantitative trait loci and environmental factors for cardiovascular disease. It is well known that genetic factors are of considerable importance for some familial lipid syndromes and that Type A Behavior pattern and increased lipid levels infer increased risk for cardiovascular disease. It is furthermore known that genetic factors are of importance levels of blood lipid biomarkers. The interplay of genetic and environmental effects for these risk factors in a normal population is less well understood and virtually unknown for the elderly. In the TwinGene project twins born before 1958 are contacted to participate. Health and medication data are collected from self-reported questionnaires, and blood sampling material is mailed to the subject who then contacts a local health care center for blood sampling and a health check-up. In the simple health check-up, height, weight, circumference of waist and hip, and blood pressure are measured. Blood is sampled for DNA extraction, serum collection and clinical chemistry tests of C-reactive protein, total cholesterol, triglycerides, HDL and LDL cholesterol, apolipo��protein A1 and B, glucose and HbA1C. The TwinGene cohort contains more than 10000 of the expected final number of 16000 individuals. Molecular genetic techniques are being used to identify Quantitative Trait Loci (QTLs) for cardiovascular disease and biomarkers in the TwinGene participants. Genome-wide linkage and association studies are ongoing. DZ twins have been genome-scanned with 1000 STS markers and a subset of 300 MZ twins have been genome-scanned with Illumina 317K SNP platform. Association of positional candidate SNPs arising from these genomscans are planned. The TwinGene project is associated with the large European collaboration denoted GenomEUtwin (www.genomeutwin.org, see below) which since 2002 has aimed at gathering genetic data on twins in Europe and setting up the infrastructure needed to enable pooling of data and joint analyses. It has been the funding source for obtaining the genome scan data. Types of samples: * EDTA whole blood * DNA * Serum Number of sample donors: 12 044 (sample collection completed) | quantitative trait loci, environmental factor, cardiovascular disease, environment, genetic, gene, lipid syndrome, lipid, health, medication, questionnaire, c-reactive protein, total cholesterol, triglyceride, hdl, ldl, cholesterol, apolipo-protein a1, apolipo-protein b, glucose, hba1c, genome-wide linkage study, genome-wide association study, genome |
is listed by: One Mind Biospecimen Bank Listing is related to: GenomEUtwin is related to: Swedish Twin Registry has parent organization: Karolisnka Biobank |
Twin | NIH ; European Union ; VR ; SSF |
nlx_151387 | http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31600&l=en | SCR_006006 | 2026-08-01 12:10:51 | 19 | ||||||
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USIDNET DNA and Cell Repository Resource Report Resource Website |
USIDNET DNA and Cell Repository (RRID:SCR_004661) | USIDNET Repository | biomaterial supply resource, material resource | The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program - the US Immunodeficiency Network - to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies / immunoglobulins, complement and other host defense mechanisms. All samples in this Repository have been de-identified to protect the privacy of the individual donors. The USIDNET also operates a Patient Data Registry in addition to this Repository and certain clinical data relating to a specific sample may be available through the Registry for some of the patient samples in the Repository collection. Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. Requestors are required to complete a Statement of Research Intent briefly describing their proposed use of materials obtained from the Repository and must sign an Assurance agreeing to conditions established by USIDNET for distribution of samples from its collection. Requestors wishing to obtain additional clinical data specific to individual samples in the Repository collection must make a separate application for that information to the Registry (see www.usidnet.org) Physicians or Patients wishing to submit cell samples for the Repository collection should first contact Coriell to arrange for the Repository to send them the correct sample collection tubes as well as prepaid mailers for returning the collected sample(s) to Coriell. Separate collection and shipping procedures may be involved depending on how many samples are to be shipped at one time and whether the shipment will involve freshly obtained blood or already established cell lines. | clinical data, dna, functional lymphoid cell, cell, lymphoid cell, blood, cell line, immunodeficiency disease, primary immunodeficiency disease |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Coriell Cell Repositories has parent organization: USIDNET: US Immunodeficiency Network |
Immunodeficiency disease | NIH | PMID:32880085 PMID:24711005 |
Public: Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. | nlx_143858 | SCR_004661 | US Immunodeficiency Network DNA Cell Repository, US Immunodeficiency Network DNA and Cell Repository, USIDNET DNA Cell Repository, US Immunodeficiency Network Repository | 2026-08-01 12:10:50 | 0 | ||||
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Roadmap Resource Report Resource Website 10+ mentions |
Roadmap (RRID:SCR_017207) | software resource, software application | Software tool to display surface of macromolecule and its properties. Uses projections to map van der Waals or solvent accessible surface of macromolecule onto plane., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Display, surface, macromolecule, property, projection, van der Waal | is related to: Purdue University; West Lafayette; Indiana | NSF ; NIH ; Medical Research Council |
PMID:8384042 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017207 | 2026-08-01 12:11:00 | 14 | ||||||||
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KI Biobank - HARMONY Resource Report Resource Website 1+ mentions |
KI Biobank - HARMONY (RRID:SCR_008884) | HARMONY | biomaterial supply resource, material resource | A twin study characterizing the importance of genetic factors for dementia and using discordant twin pairs to study other putative risk factors which control for genetic propensity to develop the disease. Molecular genetic studies have identified a number of mutations and other markers associated with early age of onset Alzheimer''''s disease. However, most cases of late age of onset dementia are considered sporadic, that is, without a clear genetic basis. Twin studies provide a unique opportunity to characterize the importance of genetic factors for dementia. Discordant twin pairs additionally provide the opportunity to study other putative risk factors which controlling for genetic propensity to develop the disease. In the first wave of the Study of Dementia in Swedish Twins, all SATSA twins born before 1935 have been screened for dementia symptoms. Over 190 suspects have been identified. This pilot study has been expanded to the entire registry in the study known as HARMONY. All twins aged 65 and older were invited to participate in a computer assisted telephone screening interview. A total of 13,519 individuals completed the interview (response rate = 75.9%). Dementia screening was based on the TELE, which includes the 10-item MSQ, other cognitive items (counting backwards, recalling three words, and similarities), and questions about health and daily functioning; or on Blessed scores obtained from a proxy interview. Among those screened, 1565 were positive for suspicion of dementia and were referred for complete clinical evaluation by a physician and a nurse. Once the preliminary in-person evaluation suggested that the suspected case was demented, the twin partner was also invited for an identical clinical work-up. Response rate for clinical evaluations is 71.4%. Approximately half of those visited for evaluation have been diagnosed as demented according to DSM-IV criteria, of which two-thirds have Alzheimer''''s disease. An extensive assessment of probable risk exposure is also included. Longitudinal follow-up is yet another feature of the study. Association studies with candidate genes are also being performed. Types of samples * DNA Number of sample donors * 1154 (sample collection completed) | interview, late adult human, clinical evaluation, association study, candidate gene, gene, risk factor, twin, longitudinal |
is listed by: One Mind Biospecimen Bank Listing is related to: Swedish Twin Registry is related to: KI Biobank - SATSA has parent organization: Karolisnka Biobank |
Dementia, Alzheimer''''s disease, Discordant twin, Aging | NIH | nlx_151298 | http://ki.se/en/meb/dementia-in-swedish-twins-harmony | SCR_008884 | Dementia in Swedish Twins (HARMONY) | 2026-08-01 12:10:42 | 2 | |||||
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Agilent: Bravo NGS Resource Report Resource Website 1+ mentions |
Agilent: Bravo NGS (RRID:SCR_019473) | instrument resource | Workstation is built on Bravo automated liquid handling robot preconfigured for library prep and target enrichment using Next-Generation Sequencing protocols. Workstation modules add microplate handling. Intuitive Agilent VWorks software enables setup of preprogrammed protocols and allows users to create custom protocols., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Agilent, NGS, Instrument Equipment | NIH U24NS120055; NIH GM137200 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_019473.pdf | SCR_019475, Model_Number_Agilent_Bravo_NGS | SCR_019473 | Agilent Bravo NGS Workstation | 2026-08-01 12:06:32 | 3 | |||||||
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ContainerProfiler Resource Report Resource Website 1+ mentions |
ContainerProfiler (RRID:SCR_023770) | software resource | Software tool supports profiling resource utilization including CPU, memory, disk, and network metrics of containerized tasks. Resource utilization metrics are obtained across three levels: virtual machine (VM)/host, container, and process. Implementation leverages facilities provided by Linux operating system that is integral with Docker containers. | Resource profiling, resource utilization, containerized tasks, resource utilization metrics, | NIH R01GM126019; NIH R01GM126019-02S2; NIH U24HG012674; NIH R03AI159286; NSF OAC-1849970 |
DOI:10.48550/arXiv.2005.11491 | Free, Available for download, Freely available | SCR_023770 | 2026-08-01 12:08:22 | 2 | |||||||||
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CompuCell3D Resource Report Resource Website 50+ mentions |
CompuCell3D (RRID:SCR_003052) | CC3D | simulation software, software resource, software application | Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior. | model, simulation, cellular, multi-cellular, windows, mac os x, linux, tissue, organ, organism, cell behavior | has parent organization: Indiana University; Indiana; USA | NIH ; EPA |
PMID:22482955 | Free, Available for download, Freely available | nlx_157668 | SCR_003052 | 2026-08-02 09:03:52 | 70 | ||||||
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Zeiss: Crossbeam 550 with Leica VCT 500 Cryo-Suite Resource Report Resource Website |
Zeiss: Crossbeam 550 with Leica VCT 500 Cryo-Suite (RRID:SCR_028555) | instrument resource | Zeiss Crossbeam 550 (sometimes referred to as the XB 550) is dual-beam system that combines the Gemini 2 SEM with the Ion-sculptor FIB (Focused Ion Beam) for advanced materials analysis and sample preparation. XB 550 combined with the Leica EM VCT 500 is a highly specialized system designed for advanced cryogenic workflows in materials and life sciences. It enables researchers to investigate and prepare samples at ultra-low temperatures without exposing them to air or contamination. | focused ion beam; FIB-SEM; electron microscope; scanning; SEM; VolumeEM; array tomography; high-resolution | is used by: University of California at Berkeley Electron Microscope Laboratory Core Facility | NIH 1S10OD030258-01 | Commercially available | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028555.pdf , https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/Leica%20SCR_028555.pdf | https://www.zeiss.com/microscopy/us/products/sem-fib-sem/fib-sem/crossbeam-550.html | SCR_028555 | , Zeiss XB 550 with Leica VCT 500 Cryo-Suite system, Berkeley EML Zeiss Crossbeam 550 with Leica VCT 500 Cryo-Suite system | 2026-08-01 12:14:48 | 0 | ||||||
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PharmKGB Resource Report Resource Website 100+ mentions |
PharmKGB (RRID:SCR_025580) | data or information resource, knowledge base | NIH-funded resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relationships. | human genetic variation affects, response to medications, clinically actionable gene-drug associations, genotype-phenotype relationships, | NIH | Free, Freely available, | SCR_025580 | Pharmacogenomics Knowledgebase | 2026-08-01 12:13:34 | 104 | |||||||||
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Caenorhabditis Genetics Center Resource Report Resource Website 1000+ mentions |
Caenorhabditis Genetics Center (RRID:SCR_007341) | CGC | cell repository, biomaterial supply resource, material resource, organism supplier | Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available. | non-human animal, caenorhabditis elegans, chromosome, database, model, mutant, nematode, nomenclature, model organism, protein, transgenic, web accessible database, genetic stock, germplasm, genotype, FASEB list |
is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: C. elegans Gene Knockout Consortium is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIH OD010440 | nif-0000-00240 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models, http://www.cbs.umn.edu/research/resources/cgc | http://biosci.umn.edu/CGC/, http://www.cgc.cbs.umn.edu | SCR_007341 | 2026-08-03 09:33:28 | 3842 | ||||||
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GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database Resource Report Resource Website 1+ mentions |
GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) | GEISHA | data repository, data or information resource, experimental protocol, database, narrative resource, atlas, storage service resource, service resource | Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA. | expression data, expression pattern, gene, gene expression, genome, chicken, chicken embryo, genomic, in situ hybridization, mapping, microarray, microrna, model organism, oligo, probe, stage, image, molecular neuroanatomy resource, embryo, embryonic chicken | has parent organization: University of Arizona; Arizona; USA | NIH ; NICHD R01HD044767 |
nif-0000-01251, r3d100012509 | https://doi.org/10.17616/R3RB6B | SCR_007440 | Gallus Expression in Situ Hybridization Analysis, GEISHA - Gallus Expression in Situ Hybridization Analysis | 2026-08-03 09:33:23 | 2 |
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