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http://nematode.lab.nig.ac.jp/

Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae

Proper citation: NEXTDB (RRID:SCR_004480) Copy   

•   Source: SciCrunch Registry

http://diademchallenge.org/data_sets.html

A software development competition, the DIADEM Challenge,to benefit the scientific community by encouraging the development of better software for automating three-dimensional reconstructions of neuronal arbors. The intent of the Sponsors is to ensure that the best software submitted for the competition is made available to the scientific community within a reasonable time and on reasonable terms. No purchase is necessary to enter or win. The competition will have two rounds. As of April 10, 2009, individuals and teams may register to participate in the competition and may download sets of image stacks (Data Sets) of non-human animal brains along with three-dimensional reconstructions for some of these Data Sets for training purposes. Submissions of software, including executable programs, supporting documentation, and reconstruction files for the Data Sets, must be uploaded to the competition website no later than April 9, 2010. In order to be eligible to win the competition, the individuals and at least one member of any teams whose submissions are selected for the Final Round (Finalists) must participate in the Final Round and scientific conference. Personal participation in the Final Round and scientific conference is important for two main reasons: first, because the Finalists software will be tested at the Final Round against additional Data Sets so that the judges can select a winner or winners, and second, because the larger scientific conference, of which the Final Round will be a part, is intended to foster extensive scientific interaction among neuroscientists and computational scientists, including plenary and poster sessions to discuss challenges, solutions, and future directions. There are 5 datasets, all of which have to be reconstructed for the qualifier phase. Once you have registered your group, dataset download information will be sent to you via E-mail. The 5 datasets are: - Cerebellar Climbing Fibers - Hippocampal CA3 Interneuron - Neocortical Layer 6 Axons - Neuromuscular Projection Fibers - Olfactory Projection Fibers Sponsors: The sponsors of this competition are: Allen Institute for Brain Science, Seattle, Washington; Howard Hughes Medical Institute (HHMI), Chevy Chase, Maryland; and Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia.

Proper citation: DIADEM Challenge: DIgital reconstruction of Axonal and DEndritic Morphology (DIADEM) Software Development Competition (RRID:SCR_008262) Copy   

•   Source: SciCrunch Registry

http://crezoo.crt-dresden.de/crezoo/

Database of helpful set of CreERT2 driver lines expressing in various regions of the developing and adult zebrafish. The lines have been generated via the insertion of a mCherry-T2A-CreERT2 in a gene trap approach or by using promoter fragments driving CreERT2. You can search the list of all transgenic lines or single entries by insertions (gene) or expression patterns (anatomy/region). In most cases the CreERT2 expression profile using in situ hybridization at 24 hpf and 48 hpf is shown, but also additional information (e.g. mCherry or CreERT2 expression at adult stages, transactivation of a Cre-dependent reporter line) is displayed. Currently, not all insertions have been mapped to a genomic location but the database will be regularly updated adding newly generated insertions and mapping information. Your help in improving and broadening the database by giving your opinion or knowledge of expression patterns is highly appreciated.

Proper citation: CreZoo (RRID:SCR_008919) Copy   

•   Source: SciCrunch Registry

https://omictools.com/l2l-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019.

Database of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: L2L Microarray Analysis Tool (RRID:SCR_013440) Copy   

•   Source: SciCrunch Registry

http://www.gudmap.org

Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system.

Proper citation: GenitoUrinary Development Molecular Anatomy Project (RRID:SCR_001554) Copy   

•   Source: SciCrunch Registry

http://cshprotocols.cshlp.org/cgi/collection/behavioral_assays

A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

Proper citation: Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays (RRID:SCR_001697) Copy   

•   Source: SciCrunch Registry

http://iscc.coh.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh.

Proper citation: Intestinal Stem Cell Consortium (RRID:SCR_001555) Copy   

•   Source: SciCrunch Registry

http://www.le.ac.uk/genetics/genie/vgec/index.html

Hub of evaluated genetics-related teaching resources for teachers and learners in schools and higher education, health professionals and the general public. Suggest or submit a learning resource to the VGEC. Resources include: * simple experiments suitable for all ages * tutorial material * videos on useful techniques * current and relevant links to other evaluated resources The Virtual Genetics Education Centre (VGEC) * Provides information and genetics education resources for higher education, colleges, schools, health professionals and the general public. * Encourages collaboration in the development, evaluation and sharing of genetics education resources * provides links to, and evaluates, sources of information and educational material about genetics. * Explores innovative approaches to teaching and learning in genetics, such as the SWIFT project for example where Second Life is being used to teach some aspects of genetics in a virtual laboratory.

Proper citation: Virtual Genetics Education Centre (RRID:SCR_001958) Copy   

•   Source: SciCrunch Registry

http://flymove.uni-muenster.de/

Database combining movies, animated schemata, interactive modules and pictures that will greatly facilitate the understanding of Drosophila development. The resource is aimed at university students and teachers of developmental biology classes. Contribute your own movies, images and illustrations to FlyMove. Illustrating developmental processes using first hand research data will allow students to gain a better understanding of the real organism, and it will allow you to draw their attention to your field of research and to your group. All donors of media integrated in FlyMove will be cited and links to their homepages will be made.

Proper citation: FlyMove (RRID:SCR_002257) Copy   

•   Source: SciCrunch Registry

http://www.gudmap.org/Resources/Ontologies.html

A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.

Proper citation: GUDMAP Ontology (RRID:SCR_002637) Copy   

•   Source: SciCrunch Registry

http://www.tarp.nih.gov/

Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.

Proper citation: Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) Copy   

•   Source: SciCrunch Registry

http://udn.nichd.nih.gov/

Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the inferotemporal gyrus, which sends projections to the amygdala, result in significant changes in the vocal behavior of infant rhesus macaques. Vocal development is a dynamic process, and a pattern shared by several nonhuman primates has emerged regarding the nature of this process. Infants are highly vocal during periods of brief separation from their caregiver, and we take advantage of this to document the range of vocalizations produced by infants of different ages. In the neonatal period, infants of 3 species of nonhuman primate (rhesus macaque, squirrel monkey and common marmoset) all produce sounds that vary widely in their acoustic structure. Many of these bear a striking similarity to sounds used in a variety of social settings by adults, suggesting that neural systems responsible for generating adult vocalizations are already in place during early infancy. As infants mature, their vocal behavior during brief periods of social separation becomes much more stereotyped. It isn't until much later in development, as individuals engage in a variety of social interactions with peers and adults, that the sounds expressed in early infancy begin to re-appear in adult contexts. The role of individual experience during development is currently being explored to determine the mechanisms leading to the acquisition of adult vocal skills.

Proper citation: NICHD Developmental Neuroethology - Laboratory of Comparative Ethology (RRID:SCR_000416) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

http://www.flybrain.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure.

Proper citation: FlyBrain (RRID:SCR_000706) Copy   

•   Source: SciCrunch Registry

http://www.morpholinodatabase.org/

Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.

Proper citation: Morpholino Database (RRID:SCR_001378) Copy   

•   Source: SciCrunch Registry

http://www.feedexp.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

Proper citation: FEED (RRID:SCR_000637) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.

Proper citation: Emory Epithelial Pathobiology Research Development Center Image Analysis Core (RRID:SCR_015909) Copy   

•   Source: SciCrunch Registry

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.

Proper citation: Emory Epithelial Pathobiology Research Development Center Gene Expression Analysis Core (RRID:SCR_015906) Copy   

•   Source: SciCrunch Registry

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.

Proper citation: Emory Epithelial Pathobiology Research Development Center Cell Culture Core (RRID:SCR_015904) Copy   

•   Source: SciCrunch Registry