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https://www.wadsworth.org/research/cores/applied-genomics

Advanced Genomic Technologies Cluster provides next-generation sequencing and Sanger sequencing. Next-generation sequencing services are provided using Illumina MiSeq and NextSeq sequencers. Services are available for amplicon re-sequencing, viral or microbial whole genome sequencing and 16S microbiome sequencing. Sanger DNA Sequencing can be performed on DNA templates such as PCR products and plasmids using ABI 3730xl and ABI3130xl instruments.

Proper citation: New York State Advanced Genomic Technology Core Facility (RRID:SCR_017687) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA).

Proper citation: regist custom genome (RRID:SCR_015999) Copy   

•   Source: SciCrunch Registry

http://www.stowers-institute.org/research/core/molecular-biology

Core services include DNA sequencing, site directed mutagenesis, genome engineering (TALENs & CRISPRS), plasmid preparations and distributing clones/vectors from in house collections. Supports real time quantitative PCR through instrument training, troubleshooting and experimental design. Stowers researchers also have access to Illumina Next Generation Sequencing technology. Constructs libraries, performs sequencing and assists with high throughput genome sequencing, RNA-seq and ChIP-seq projects. Utilizes liquid handling and colony manipulation robots to automate many of services. Provides automation expertise and collaborate with researchers on custom automation projects.

Proper citation: Stowers Institute for Medical Research Molecular Biology Core Facility (RRID:SCR_017776) Copy   

•   Source: SciCrunch Registry

https://med.miami.edu/centers-and-institutes/hihg/research-centers/center-for-genome-technology/biorepository-core

Core provides services and houses samples collected over the last 30 years. Biorepository processes, archives, and retrieves biological samples for genomic research. Offers variety of sample processing options including but not limited to automated DNA extraction using Autogen FLEXSTAR+ instrument, automated DNA/RNA extraction using Qiagen QIASymphony, peripheral blood mononuclear cell (PBMC) isolation, serum, plasma and buffy coat isolation, creation of blood cards, DNA/RNA quantitation and qualitation, whole genome amplification, cell-line lymphoblast immortalization and primary fibroblast tissue culture. Offers sample solutions tos uit customized needs.Services also include DNA/RNA Extraction,Sample archiving, retrieval and allocation,Unique and custom labels printing,DNA/RNA quantitation and qualitation,Tissue culture,Whole genome amplification.

Proper citation: University of Miami Hussman Institute for Human Genomics Biorepository Core Facility (RRID:SCR_017816) Copy   

•   Source: SciCrunch Registry

https://med.miami.edu/centers-and-institutes/hihg/research-centers/center-for-genome-technology/sequencing-core

Core Facility offers services utilizing Illumina Novaseq X Plus, Pacific Biosciences Revio, ONT Promethion, and 10x Genomics platforms. The core has extensive knowledge of DNA/RNA library preparation for short-read, long-read and single cell sequencing. Sample preparation is fully automated on Perkin Elmer robotic workstations and tracked via the Clarity LIMS. Services include, but are not limited to, whole genome, exome and custom capture protocols, as well as, bulk RNAseq, small RNAseq, and single cell RNA sequencing.

Proper citation: University of Miami Hussman Institute for Human Genomics Sequencing Core Facility (RRID:SCR_017828) Copy   

•   Source: SciCrunch Registry

http://gif.biotech.iastate.edu/

Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects.

Proper citation: Iowa State University Genome Informatics Core Facility (RRID:SCR_017790) 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://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html

Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.

Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy   

•   Source: SciCrunch Registry

https://blobtoolkit.genomehubs.org/blobtools2/

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

Proper citation: BlobTools2 (RRID:SCR_023351) Copy   

•   Source: SciCrunch Registry

http://www.fugu-sg.org/

THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.

Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy   

•   Source: SciCrunch Registry

https://genome-cancer.ucsc.edu/

A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.

Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy   

•   Source: SciCrunch Registry

http://www.unil.ch/comparativegenometrics/

The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids.

Proper citation: Comparative Genometrics (RRID:SCR_012920) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/D_rerio/

Database of zebrafish genome.

Proper citation: Zebrafish Genome Project (RRID:SCR_013157) Copy   

•   Source: SciCrunch Registry

http://www.treefam.org

A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics

Proper citation: Tree families database (RRID:SCR_013401) Copy   

•   Source: SciCrunch Registry

http://www.cdtdb.brain.riken.jp/CDT/Top.jsp

Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.

Proper citation: Cerebellar Development Transcriptome Database (RRID:SCR_013096) Copy   

•   Source: SciCrunch Registry

http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

•   Source: SciCrunch Registry

http://proline.bic.nus.edu.sg/dedb/

Database on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.

Proper citation: Drosophila melanogaster Exon Database (RRID:SCR_013441) Copy   

•   Source: SciCrunch Registry

http://toxodb.org/toxo/

A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info

Proper citation: ApiDB ToxoDB (RRID:SCR_013453) Copy   

•   Source: SciCrunch Registry

http://www.echinobase.org/

Database that provide a genomic information and comparative genomics platform on sea urchins and related echinoderms. It provide collection of information to directly support experimental work on these useful research models in cell and developmental biology.

Proper citation: EchinoBase (RRID:SCR_013732) Copy   

•   Source: SciCrunch Registry