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http://blocks.fhcrc.org/blocks/codehop.html

This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) Copy   

•   Source: SciCrunch Registry

http://neibank.nei.nih.gov

An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank.

Proper citation: NEIBank (RRID:SCR_007294) Copy   

•   Source: SciCrunch Registry

http://coot.embl.de/g2d/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.

Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy   

•   Source: SciCrunch Registry

https://hirnetwork.org

Network helps to organize and support collaborative research related to loss of functional beta cell mass in Type 1 Diabetes (T1D). Project consists of four independent research initiatives: Consortium on Beta Cell Death and Survival (CBDS), Consortium on Human Islet Biomimetics (CHIB), Consortium on Modeling Autoimmune Interactions (CMAI), Consortium on Targeting and Regeneration (CTAR), and Human Pancreas Analysis Program (HPAP).

Proper citation: Human Islet Research Network (HIRN) (RRID:SCR_014393) Copy   

•   Source: SciCrunch Registry

https://www.kaggle.com/rramele/p300samplingdataset

Dataset replicating the experiment done on BNCI-HORIZON 008-2014 dataset. BCI P300 Speller Kaggle Dataset for Healthy subjects

Proper citation: P300-Dataset (RRID:SCR_015977) Copy   

•   Source: SciCrunch Registry

https://dna-analysis.yale.edu/

Core supports DNA Sequencing of PCR, Plasmid, BAC and Fosmid templates, Fragment Analysis of Microsatellites, AFLP, t-RFLP, SHAPE Experiments and Human Cell Line Authentication.

Proper citation: Yale University DNA Analysis on Science Hill Core Facility (RRID:SCR_017689) Copy   

•   Source: SciCrunch Registry

http://cancer.northwestern.edu/research/shared-resources/pathology-core-facility.html

Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking.

Proper citation: Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility (RRID:SCR_017769) Copy   

•   Source: SciCrunch Registry

http://www.einstein.yu.edu/departments/genetics/resources/molecular-cytogenetics-core.aspx

Core provides tools for preparation of human and murine samples suitable for molecular genetic and cytogenetic analysis of entire genome. These tools include establishment of EBV transformed cell lines; isolation of DNA and mRNA from variety of tissue culture samples as well as primary biopsies; preparation of metaphase chromosomes suitable for fluorescence in situ hybridization (FISH) and Spectral Karyotyping (SKY) or whole chromosome paints for human and mouse genome. Core personnel is trained to hybridize commercial probes and to designed locus specific probes for regions of interest to investigators. All probes are custom designed and in house generated.

Proper citation: Albert Einstein College of Medicine Molecular Cytogenetics Core Facility (RRID:SCR_017815) Copy   

•   Source: SciCrunch Registry

http://neuralsci.org/neuracell

Core facility provides neural stem cells (NSC) and everything you need to grow them, custom lentiviral shRNA and over-expression vectors, consult based characterization service where we can assess how your products or reagents affect stem cell performance and behavior. Services include:Cell Supply,Adult SVZ Neural Stem Cells,Any Age Embryonic stem cells from any region of the brain,Human Retinal Pigmented Epithelial cells,RPE iPSCs,iPSCs,Neural Progenitor Cells (NPCs),Custom Orders,Media/ Dissociation Reagents,High-performance Media formulated according to optimal cell growth conditions,Complete Defined Media for Neural Stem Cell Culture,Complete Defined Media for Human Retinal Pigmented Epithelial Culture,Cell characterization. Performs assays to verify how stem cell populations behave in response to certain environments, plastics, reagents, etc., using trade secret assays via FACS and cell culture techniques. This can be used for neural stem cells as well as embryonic stem cells.Cell banking solutions shall ensure that their integrity is maintained, and that sufficient supply is readily available. We will also expand cells, harvest cells, generation the freezing medium and thaw cells to test performance. Provides Generation of custom lentiviral shRNA constructs,Generation of custom lentiviral over-expression constructs,Supply of NSC lines already expressing these shRNA or over-expression constructs.

Proper citation: Neural Stem Cell Institute NeuraCell Core Facility (RRID:SCR_017821) Copy   

•   Source: SciCrunch Registry

http://omrf.org/research-faculty/core-facilities/human-antibody-core-facility/

Core produces fully human, full length, antigen specific antibodies for use in studying human immune responses. Produces high affinity protective antibodies to influenza, anthrax lethal toxin, and various S. pneumonia polysaccharides. Helps quantify antibody secreting cell responses after vaccination and by generating human monoclonal antibodies to be characterized. Pathogen specific human monoclonal antibodies are also available for licensing agreements and other forms of commercial development. Services include to define temporal human immune responses after vaccination and to generate human monoclonal antibodies to supplement research,development of novel methods to produce human monoclonal antibodies after acute infection and other immune events, investigation of new technologies for characterization of human monoclonal antibodies produced by core.

Proper citation: Oklahoma Medical Research Foundation Human Antibody Core Facility (RRID:SCR_017795) Copy   

•   Source: SciCrunch Registry

http://htbc.stanford.edu

Core provides fully automated high throughput screening (HTS) of Compound Libraries (130,000+ compounds) for both enzyme/protein-based assays and cell-based assays, using Caliper Life Sciences Staccato system;Genomic siRNA screening with siARRAY whole human genome siRNA library from Dharmacon targeting 21,000 genes, using Agilent Bravo system;High-Content Screening using ImageXpress Micro automated fluorescent microscope with live cell, bright field, phase contrast and integrated plate handling with Thermo Catalyst CRS, and image analysis using MetaXpress software;High Throughput Molecular Biology reagents and services, including access to cDNA libraries (Human ORFeome collection, 15,000 genes) and 96 and 384-well bead clean-ups and PCR setup (Biomek FX and Agilent Bravo), and other automation steps in collaboration with SFGF;High-throughput assay development assistance with cell culture, experiment design, robotic programming and Standard Operating Procedure drafting;Screening data analysis assistance with protocols, hit determination and structure activity analyses using MDL chemical database ISIS/HOST, Plate Manager, Assay Explorer and Report Manager. Use of microplate reader detection systems, including Tecan Infinite M1000 and Infinite M1000 PRO and Molecular Devices Analyst GT for fluorescence; fluorescence polarization; time-resolved fluorescence; absorbance and luminescence (with injectors and AlphaScreen); and Flexstation II 384, for kinetic fluorescence reads to measure calcium mobilization and ion channels.Use of liquid-handling robots, including Sciclone ALH3000 (96- and 384-well pipetting), Agilent Bravo (96- and 384-well pipetting), Velocity11 VPrep (96-well pipetting), Bio-Tek plate washers/dispensers, Matrix Wellmate and Titertek/Labsystems Multidrop microplate dispensers, and Velocity11 PlateLoc plate heat sealer;Training for most of these services.

Proper citation: Stanford University School of Medicine High Throughput Bioscience Center Core Facility (RRID:SCR_017794) Copy   

•   Source: SciCrunch Registry

https://him.uchicago.edu/

Facility serves as specialized laboratory performing correlative assays for cancer-based clinical trials. Participates in project development to assist in assay selection and optimization prior to study initiation. Offers pick-up service for specimens from patients at U of C Hospital or outpatient clinics, and process samples as indicated for assays being performed. For some studies, isolation and freezing of peripheral blood lymphocytes for analysis at later date is performed, while for others immediate staining of whole blood for specific cell surface markers of interest is carried out. Prepares clinical grade products, such as peptide vaccines, for administration into patients.Assays performed include ELISA, ELISPOT, tetramer binding assays, detection of cell surface markers by flow cytometry, and biochemical assays such as Western Blots, RNA extraction from tumor biopsies and either real time RT-PCR for specific transcripts or preparation of samples for gene expression profiling. Facility is equipped with MACSQuant Flow Cytometer, ELISA microplate reader, ELISPOT reader, PCR thermocyclers, CO2 incubators, biosafety cabinets, centrifuges, and equipment for Western blot analysis. Performs assays on human samples but consideration will be given to expanding these services to mouse-model systems.

Proper citation: University of Chicago Human Immunologic Monitoring Core Facility (RRID:SCR_017916) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/center-biospecimen-research-development

Core mission is to drive scientific discovery through use of human specimens.Helps facilitate translational research, match human specimen resources to scientific needs, foster multi-investigator collaborative projects, and catalyze scientific innovation,improving researcher access to existing biospecimen resources, and enhancing institution-wide tissue-banking efforts and capacity. Another priority is to implement campus-wide policy for human biospecimen collection and storage to ensure regulatory compliance.

Proper citation: New York University School of Medicine Langone Health Center for Biospecimen Research and Development Core Facility (RRID:SCR_017930) Copy   

•   Source: SciCrunch Registry

http://hormone.facilities.northwestern.edu

Core provides hormone analyses for both human and animal studies for scientific community at Northwestern, small rodent metabolic phenotyping resources for diabetes, obesity and other metabolic research.Maintains quality control and standardize internal references for hormone assays.Maintains reference database information on mouse metabolic phenotyping models from Northwestern University community.Services include:Immunoassays for endocrine hormones, assays using technology from Luminex,Lipid and glucose chemical analyeses,Roche Cobas e 411 analyzer employing sophisticated electrochemiluminescence (ECL) technology to deliver excellent low-end sensitivity and broad dynamic range of assays including metabolic and reproductive hormones, thyroid function test, cardiac markers, maternal care, tumor markers and bone turnover markers.,TSE LabMaster Automated Phenotyping system is a state-of-the-art system for studying energy metabolism at whole animal level.

Proper citation: Northwestern University Comprehensive Metabolic Core Facility (RRID:SCR_017871) Copy   

•   Source: SciCrunch Registry

http://www.mskcc.org/research/molecular-cytogenetics

Core supports cytogenetic analysis of cells from human and research animal sources. Range of chromosome analysis techniques are ranging from basic G-banded karyotyping, to 24-color Spectral Karyotyping (SKY), as well as Fluorescence in situ Hybridization (FISH) mapping of cloned DNAs.Services include:Karyotype characterization of new cell lines,Confirmation of cell line identity or stability,Karyotype screening of ES cells prior to transgenesis,Mapping of transgene integration sites,Chromosome or locus copy number enumeration,Publication-quality illustrations.Cytogenetic techniques available:Short-term cell culture,Metaphase chromosome preparation,G-banded karyotyping.FISH techniques available:DNA labeling for custom probe generation (for FISH projects),DNA amplification by DOP-PCR,Chromosome painting,FISH mapping (on chromosomes, interphase nuclei or DNA fibers),Tissue FISH (paraffin or frozen sections),Immuno-FISH (DNA FISH combined with fluorescent immunostaining) , Spectral karyotyping (SKY),Q-FISH (measurement of telomere lengths).

Proper citation: Memorial Sloan Kettering Cancer Center Molecular Cytogenetics Core Facility (RRID:SCR_017850) Copy   

•   Source: SciCrunch Registry

http://hihg.med.miami.edu/cgt/gene-expression

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip.

Proper citation: University of Miami Miller School of Medicine Gene Expression Core Facility (RRID:SCR_017825) Copy   

•   Source: SciCrunch Registry

http://www.hcp.med.harvard.edu/ncs/

The baseline NCS, fielded from the fall of 1990 to the spring of 1992, was the first nationally representative mental health survey in the U.S. to use a fully structured research diagnostic interview to assess the prevalences and correlates of DSM-III-R disorders. The baseline NCS respondents were re-interviewed in 2001-02 (NCS-2) to study patterns and predictors of the course of mental and substance use disorders and to evaluate the effects of primary mental disorders in predicting the onset and course of secondary substance disorders. In conjunction with this, an NCS Replication survey (NCS-R) was carried out in a new national sample of 10,000 respondents. The goals of the NCS-R are to study trends in a wide range of variables assessed in the baseline NCS and to obtain more information about a number of topics either not covered in the baseline NCS or covered in less depth than we currently desire. A survey of 10,000 adolescents (NCS-A) was carried out in parallel with the NCS-R and NCS-2 surveys. The goal of NCS-A is to produce nationally representative data on the prevalences and correlates of mental disorders among youth. The NCS-R and NCS-A, finally, are being replicated in a number of countries around the world. Centralized cross-national analysis of these surveys is being carried out by the NCS data analysis team under the auspices of the World Health Organization (WHO) World Mental Health Survey Initiative. In order to provide an easily accessible database which can be updated and checked on a regular basis, we have created a public use file system containing all the documents from the NCS and NCS-R programs. These file systems can be accessed through the Internet and either downloaded onto a disk or printed. We will update the system on a regular basis to add newly completed paper abstracts and other documents. In addition, the NCS and NCS-R data can be accessed through ICPSR (Inter-university Consortium for Political and Social Research). Any updates to the data to correct coding or classification errors will be made available along with written documentation of the changes in ICPSR''s quarterly newsletter.

Proper citation: National Comorbidity Survey (RRID:SCR_004588) Copy   

•   Source: SciCrunch Registry

http://www.brighamandwomens.org/Departments_and_Services/radiology/Research/BRIC/default.aspx

Imaging Core facility that provides a comprehensive research imaging service to meet the needs of investigators and research subjects using imaging facilities at Brigham and Women's Hospital (BWH). A unique feature of BRIC is the complete anonymity of research subjects. Research image scheduling, image acquisition and image storage are all kept completely separate from BWH clinical Radiology systems. The BRIC provides the administrative infrastructure, customer service architecture and institutional support to promote investigative applications of imaging technologies.

Proper citation: BWH Research Imaging Core (RRID:SCR_002708) Copy   

•   Source: SciCrunch Registry

http://eyebrowse.cit.nih.gov/

EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation.

Proper citation: EyeBrowse (RRID:SCR_008000) Copy   

•   Source: SciCrunch Registry

http://www.hgvs.org/dblist/dblist.html

A list of various databases freely available to the public, including several mutation and variation resources, such as education resources for teachers students provided by the Human Genome Variation Society. Databases listed include: * Locus Specific Mutation Databases * Disease Centered Central Mutation Databases * Central Mutation and SNP Databases * National and Ethnic Mutation Databases * Mitochondrial Mutation Databases * Chromosomal Variation Databases * Other Mutation Databases ( i.e. your round holes don''''t fit our square pegs) * Clinical and Patient Aspects Databases * Non Human Mutation Databases * Artificial Mutations Only * Other Related Databases * Education Resources for Teachers and Students

Proper citation: Human Genome Variation Society: Databases and Other Tools (RRID:SCR_006876) Copy   

•   Source: SciCrunch Registry