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http://www.genomesize.com

Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff.

Proper citation: Animal Genome Size Database (RRID:SCR_007551) Copy   

•   Source: SciCrunch Registry

http://gene3d.biochem.ucl.ac.uk/Gene3D/

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gene3D (RRID:SCR_007672) Copy   

•   Source: SciCrunch Registry

http://genomics.senescence.info/

Collection of databases and tools designed to help researchers study the genetics of human ageing using modern approaches such as functional genomics, network analyses, systems biology and evolutionary analyses. A major resource in HAGR is GenAge, which includes a curated database of genes related to human aging and a database of ageing- and longevity-associated genes in model organisms. Another major database in HAGR is AnAge. Featuring over 4,000 species, AnAge provides a compilation of data on aging, longevity, and life history that is ideal for the comparative biology of aging. GenDR is a database of genes associated with dietary restriction based on genetic manipulation experiments and gene expression profiling. Other projects include evolutionary studies, genome sequencing, cancer genomics, and gene expression analyses. The latter allowed them to identify a set of genes commonly altered during mammalian aging which represents a conserved molecular signature of aging. Software, namely in the form of scripts for Perl and SPSS, is made available for users to perform a variety of bioinformatic analyses potentially relevant for studying aging. The Perl toolkit, entitled the Ageing Research Computational Tools (ARCT), provides modules for parsing files, data-mining, searching and downloading data from the Internet, etc. Also available is an SPSS script that can be used to determine the demographic rate of aging for a given population. An extensive list of links regarding computational biology, genomics, gerontology, and comparative biology is also available.

Proper citation: Human Ageing Genomic Resources (RRID:SCR_007700) Copy   

•   Source: SciCrunch Registry

http://mousebiology.org

Core located on campus of UC Davis, providing fully customized support for scientific research using genetically altered mice. Provides access to develop, plan, execute, and analyze research project involving genetically-altered mice. Provides description of project, including alternative approaches, accurate timelines, and cost estimates.Provides regular and informative communication throughout project, including email updates on completion of each milestone. Project progress can be followed at each stage by viewing detailed information anytime by accessing our online and secure project tracking system (PTS) available 24 hours a day.

Proper citation: University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility (RRID:SCR_017851) 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://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://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://med.nyu.edu/research/scientific-cores-shared-resources/genome-technology-center

Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results.

Proper citation: New York University School of Medicine Langone Health Genome Technology Center Core Facility (RRID:SCR_017929) Copy   

•   Source: SciCrunch Registry

https://grcf.jhmi.edu/

Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms.

Proper citation: Johns Hopkins University School of Medicine Genetic Resources Core Facility (RRID:SCR_018669) Copy   

•   Source: SciCrunch Registry

http://cccb.dfci.harvard.edu

Core facility that provides the following services: Microarray and other genomic data analysis, MiSeq. The Center provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research. The CCCB has three primary elements. * The CCCB sequencing facility offers a wide range of services to assist in the design and execution of next-generation sequencing projects. Utilizing the Illumina (Solexa) sequencing technology, they currently support a number of applications inlcuding ChIP-Seq, RNA-Seq, whole genome, whole exome, and targeted re-sequencing. * The analytical services and support platform aims to provide state-of-the-art assistance in the collection, management, analysis, and interpretation of large-scale data with a focus on data generated using ''''omic technologies. In addition, they offer software, services, and training designed to assist investigators in advancing their research. * The CCCB research program is focused on development of new methods for improving analysis and interpretation of genomic data through integration of diverse data types with the goal of creating open-source software tools to be made freely-available to the research community.

Proper citation: DFCI Center for Cancer Computational Biology (RRID:SCR_012688) Copy   

•   Source: SciCrunch Registry

https://einsteinmed.edu/research/shared-facilities/cores/53/epigenomics/

Part of Einstein Center for Epigenomics and Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and number of assays to study the genome/epigenome. Data analytical services are provided by Computational Genomics Facility.

Proper citation: Albert Einstein College of Medicine Epigenomics Shared Core Facility (RRID:SCR_023284) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/sites/batchentrez

Software program for loading numbers of genome records. Allows the retrieval of a large number of nucleotide sequences or protein sequences, in a batch mode, by importing a file containing a list of the desired GI or accession numbers.

Proper citation: Batch Entrez (RRID:SCR_016634) Copy   

•   Source: SciCrunch Registry

https://www.integromics.com/omicsoffice-for-ngs/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

Proper citation: OmicsOffice for NGS SeqSolve (RRID:SCR_001222) Copy   

•   Source: SciCrunch Registry

https://github.com/huangnengCSU/compleasm

Software genome completeness evaluation tool based on miniprot.

Proper citation: compleasm (RRID:SCR_026370) Copy   

•   Source: SciCrunch Registry

https://github.com/YongyiLuo98/BVSim

Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum.

Proper citation: BVSim (RRID:SCR_026926) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/SlideTags_Pipeline/README

Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification.

Proper citation: SlideTags.wdl (RRID:SCR_027567) Copy   

•   Source: SciCrunch Registry