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http://linux1.softberry.com/spldb/SpliceDB.html

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.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry

http://aws.amazon.com/1000genomes/

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

Proper citation: 1000 Genomes Project and AWS (RRID:SCR_008801) Copy   

•   Source: SciCrunch Registry

https://www.unmc.edu/vcr/cores/vcr-cores/mgec/index.html

Core Facility provides expertise and advice for experimental design of transgenic or gene knockout experiments, including DNA construct production and genotyping assays, makes reagents available for generation of transgene or gene targeting constructs, and performs all experimental aspects, which include pronuclear injection of transgene constructs, generation of recombinant mouse ES cells, blastocyst injection, and embryo transfer surgeries, for generation or rederivation of genetically manipulated mouse strains. Transgenic founder mice or chimeric animals with targeted alleles are then transferred to individual investigator for analysis.

Proper citation: Nebraska University Medical Center Mouse Genome Engineering Core Facility (RRID:SCR_017755) Copy   

•   Source: SciCrunch Registry

http://einstein.yu.edu/shRNA

Core Facility was closed in November 2016. Services of shRNA Core were redistibuted to other existing facilities at Einstein.Gene Modulation Services: CRISPR, RNAi and ORF. CRISPR-Cas9 services for cell lines will now be performed in Gene Modification Facility. Gene Modification Facility already offers CRISPR services for genetic modification of mice and will utilize this scientific expertise to provide CRISPR services for the gene modification of cell lines as well. You can access these services through core's site in iLab.The human and mouse whole genome shRNA library has been relocated to the Molecular Cytogenetic Core. The core staff will pull requested shRNA and ORF clones from our collection for investigators. You can access this service through the core's site in iLab.Access and operation of the Operetta instrument for high-content imaging will now be coordinated through the Macromolecular Therapeutics Development Facility (MTDF). You can access this service through the core's site in iLab. Lentivirus prep from shRNA and CRSPR constructs can be obtained from our Gene Therapy Core from clones obtained from the Molecular Cytogenetic Core. You can access this service through the core's site in iLab.

Proper citation: Albert Einstein College of Medicine shRNA Core Facility (RRID:SCR_017846) Copy   

•   Source: SciCrunch Registry

https://ki.mit.edu/sbc/escell

Core provides service support to all MIT investigators who utilize specialized in vitro cells such as stem cells, organoids, or primary cell lines and/or novel mouse models to study human diseases such as cancer. Projects involve generation of new model system, such as CRISPR-mediated gene editing in mouse to introduce mutation that mimics one found in patients. Helps with projects required optimization of finicky cell cultures and other challenges.Provides customizable set of service options to match specific needs of each project, including consultative advice and troubleshooting, complete tissue culture and microinjection services within our facilities or hands-on training to enable investigators to perfom these experiments either at their own laboratory or within our facilities.Services Include:Gene Targeting genomic modification through traditional or CRISPR/Cas9 locus targeting, assistance with targeting strategies and vector designs;Embryonic Stem Cells generation of new ES lines from mouse strains, importation and testing of lines from outside sources, differentiation of ES lines into specific cell lineages or cell types and more;Microinjection injection of mouse ES cells into blastocysts to generate chimeras and injection of DNA, RNA or CRISPR RNPs into the pronucleus of fertilized mouse eggs to generate transgenic and edited mice;Specialized Tissue Culture establishemnt of new primary cell cultures from a tumor, tissue or organ; Isolation of fibroblasts (MEFs) from mice for culture and analysis;Tissue Culture for Xenograft and Syngenic Modeling optimization, validation and testing of cell lines for orthotopic placement into mice, coordinated with Preclinical Testing Facility;Repository of Reagent Mice Commonly used wild type mice such as C57BL/6j as well as KrasG12D-based models of cancers are maintained on campus for efficient distrubution;Training and Troubleshooting for all aspects of embryonic stem cells, primary cultures, animal breeding etc.;Serum, DMEM, LIF and other media components that have been tested and verified for use with ES cells.

Proper citation: Massachusetts Institute of Technology Koch Institute Preclinical Modeling Core Facility (RRID:SCR_017899) Copy   

•   Source: SciCrunch Registry

http://ssom.luc.edu/genomics/

Core provides next-generation sequencing capabilities using Illumina MiSeq. Helps with experimental design, quality control analysis, library preparation, and data analysis. MiSeq desktop sequencer allows to access applications such as targeted gene sequencing, metagenomics, small genome sequencing, targeted gene expression, amplicon sequencing, and HLA typing.MiSeq is capable of delivering up to 15 Gb of output with 25 million sequencing reads and 2x300 basepair read lengths.

Proper citation: Loyola University Genomics Core Facility (RRID:SCR_017857) Copy   

•   Source: SciCrunch Registry

http://www.uwtransgenics.org/

Core facility that creates transgenic and gene-targeted mice using pronuclear microinjection, targeted ES cell microinjection, and CRISPR/Cas9 gene editing. Offers mouse rederivation services to create specific pathogen free mice or to rederive cryopreserved mouse lines. Additionally, embryo and sperm cryopreservation services are available to provide long-term storage of valuable mouse strains or stocks. Services include:Pronuclear Microinjection,ES Cell Microinjection,ES Cell Electroporation CRISPR/Cas9,In Vitro Fertilization,Sperm Cryopreservation,Embryo Cryo,Embryo Rederivation.

Proper citation: University of Washington Transgenic Resources Program Core Facility (RRID:SCR_017863) Copy   

•   Source: SciCrunch Registry

http://www.salk.edu/science/core-facilities/integrative-genomics-and-bioinformatics-core/

Core facility established to assist the Salk community with integrating genomics data into their research. The primary focus of the core is to provide analysis support for next-generation sequencing applications.

Proper citation: Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842) Copy   

•   Source: SciCrunch Registry

https://sc.edu/study/colleges_schools/pharmacy/research_and_practice/research_centers_and_facilities/functional_genomics_core/index.php

Core offers resources and solutions for conducting genomics, transcriptomics, epigenomics and functional genomics projects. We work with researchers to determine project goals and design custom solutions. We assist at all stages of the project, from support in grant development to generation of publication-quality data. Services include Consultations, Bioinformatics, Nucleic Acids purification, quantification and QC DNA Sequencing (SANGER and NGS), Library Constructions for NGS applications,Microarray Hybridization, Real Time PCR, Custom epigenomics applications, Lentiviral vectors and lentiviruses construction and production, CRIPR-CAS9sgRNAs and RNAi/shRNAs knockdown of individual genes and functional screening of sgRNA and shRNA libraries for target identification.

Proper citation: University of South Carolina Functional Genomics Core Facility (RRID:SCR_026178) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/babelgene/index.html

Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ).

Proper citation: babelgene (RRID:SCR_027117) Copy   

•   Source: SciCrunch Registry

http://pfs.nus.edu.sg/(S(dyrcwejlfws33vxe23zlvrf3))/CopyRightNotice.aspx?ReturnURL=%2fQueryInterface_V5_2.aspx

Search engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions.

Proper citation: pfSNP (RRID:SCR_002167) Copy   

•   Source: SciCrunch Registry

http://www.humgen.rwth-aachen.de/

Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges.

Proper citation: Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) Copy   

•   Source: SciCrunch Registry

http://genome.jgi.doe.gov/

Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.

Proper citation: JGI Genome Portal (RRID:SCR_002383) Copy   

•   Source: SciCrunch Registry

https://www.genevestigator.com/gv/

A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.

Proper citation: Genevestigator (RRID:SCR_002358) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

http://reflect.embl.de/

Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community.

Proper citation: Reflect (RRID:SCR_002714) Copy   

•   Source: SciCrunch Registry

http://camera.calit2.net/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Proper citation: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) Copy   

•   Source: SciCrunch Registry

http://www.g2conline.org/

Genes to Cognition (G2C) Online is about modern neuroscience. It focuses on cognitive disorders, cognitive processes, and research approaches. Use the dynamic network maps to explore our library of 750+ unique items. Or, use the linear Selected Items menu on top of each map to tour selected content. Read the G2C blog, use simple mapper, or the 3-D brain, an interactive model of the brain. Disorders included in this site: ADHD, Alzheimer's Disease, Autism, Bipolar Disorder, Depression, Schizophrenia Cognitive Processes include: Attention, Language, Learning and Memory, Perception, and Thinking Research Approaches include: Bioinformatics, Ethics, Gene Finding, Model systems, Neuroimaging, Psychology. Navigation: Interact with the dynamic Networks Maps to explore the full catalog of content. Roll-over a node on the map for a preview and click to open the content. Move on to other content by returning to the network map. Each node you visit on the map gets flagged. Follow the Selected Items Subway Line for an overview of a topic. Roll-over a subway node for a preview and click to open the content. Other Features: Most content items include links to Related Items, which allow you to explore further. The Glossary includes over 300 neuroscience keywords. Search for content using keywords or id number. Select a preferred network map to view the content in context. Open/close the History at the lower left to view visited content. Your history is stored until you clear it. Simple Mapper - We developed Simple Mapper to power this web site on the brain. Now, you can use it to organize what comes out of yours! With Simple Mapper create and save concept maps, network diagrams, or flowcharts for personal use or to share with others. 3-D Brain - The G2C Brain is an interactive 3-D model of the brain, with 29 structures that can be rotated in three-dimensional space. Each structure has information on brain disorders, brain damage, case studies, and links to modern neuroscience research. Ideal for students, researchers, and educators in psychology and biology. Also available for download: 3D Brain App for iPhone and iPod Touch!

Proper citation: Genes to Cognition Online (RRID:SCR_002746) Copy   

•   Source: SciCrunch Registry

http://sherlock.ucsf.edu/

Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes.

Proper citation: Sherlock (RRID:SCR_001628) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/rseqdiff/

An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing.

Proper citation: rSeqDiff (RRID:SCR_001683) Copy   

•   Source: SciCrunch Registry