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http://margalit.huji.ac.il/promec/

A compilation of E. coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E. coli chromosome, as well as the actual sequences in the promoter region. The database is currently updated as of July 2000 and includes 471 entries.

Proper citation: PromEC (RRID:SCR_013514) Copy   

•   Source: SciCrunch Registry

http://www.kazusa.or.jp/huge/

The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.

Proper citation: HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) Copy   

•   Source: SciCrunch Registry

http://www.simbiome.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 18, 2015. Simbiome is a curated, online electronic resource that organizes and presents relevant resources for physics-based simulation of biomedical structures and related entities in biology and life sciences.

Proper citation: Simbiome (RRID:SCR_013640) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/striatalvoimap/

An atlas intended to provide accurate data in terms of specific uptake location to make the BP quantitation. The VOIs were manually drawn with software Analyze 9.0 (Mayo Clinic) in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template. Each striatum was divided into 6 sub-regions: ventral caudate, anterior dorsal caudate, posterior dorsal caudate, ventral putamen, anterior dorsal putamen and posterior dorsal putamen.

Proper citation: Striatal Subregional VOImap (RRID:SCR_014173) Copy   

•   Source: SciCrunch Registry

http://viroligo.okstate.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR.

Proper citation: VirOligo: Virus Oligonucleotide Database (RRID:SCR_013481) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cmap/

The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub).

Proper citation: Brain Coactivation Map (RRID:SCR_014172) Copy   

•   Source: SciCrunch Registry

http://www.phenogo.org

PhenoGO is a computed database designed for high throughput mining that provides phenotypic and experimental context - such as the cell type, disease, tissue, and organ - to existing annotations between gene products and Gene Ontology (GO) terms, as specified in the Gene Ontology Annotations (GOA) for multiple model organisms. Phenotypic and Experimental (P&E) contexts to identifiers are computationally mapped to general biological ontologies, including: the Cell Ontology (CO), phenotypes from the Unified Medical Language System (UMLS), species from Taxonomy of the National Center for Biotechnology Information (NCBI) taxonomy, and specialized ontologies such as Mammalian Phenotype Ontology (MP) and Mouse Anatomy (MA).

Proper citation: PhenoGO (RRID:SCR_013646) Copy   

•   Source: SciCrunch Registry

http://rose.man.poznan.pl/aars/index.html

The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable.

Proper citation: Aminoacyl-tRNA synthetase database (RRID:SCR_013498) Copy   

•   Source: SciCrunch Registry

http://www.lsbm.org/site_e/database/index.html

It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides

Proper citation: SBM DB (RRID:SCR_013491) Copy   

•   Source: SciCrunch Registry

http://www.wormguides.org/home

A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase.

Proper citation: WormGUIDES (RRID:SCR_013733) Copy   

•   Source: SciCrunch Registry

http://lablog.sourceforge.net

An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering.

Proper citation: LabLog (RRID:SCR_013975) Copy   

•   Source: SciCrunch Registry

http://rarge.psc.riken.jp/rartf/

Database of complete sets of Arabidopsis transcription factors with a variety of information on Arabidopsis thaliana transcription factor families including: full-length cDNA sequences, Ds-tagged mutants, multiple sequences alignments of family members, phylogenic trees, functional motifs, and so on. In addition, expression profiles of all transcription factor genes are available.

Proper citation: RARTF (RRID:SCR_013457) 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

https://www.labfolder.com

An ELN (electronic lab notebook) software application where researchers can record and organize their data by recording, dragging, and dropping elements. Users can utilize tools and features such as image annotation, search and filter, protocol templates, and team communication. The format of the ELN is customizable and can be rearranged at any point.

Proper citation: labfolder (RRID:SCR_013974) Copy   

•   Source: SciCrunch Registry

http://www.lamondlab.com/NOPdb/

It archives data on more than 700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene its domain structures and relevant protein homologues across species as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints highlighted by visualization means in the NOPdb provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/ uncharacterized proteins. The NOPdb is searchable by either gene names protein sequences Gene Ontology terms or motifs or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink OMIM and PubMed).

Proper citation: NoPdb: Nucleolar Proteome Database (RRID:SCR_013459) Copy   

•   Source: SciCrunch Registry

http://db.systemsbiology.net/kaviar/

A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.

Proper citation: KAVIAR (RRID:SCR_013737) Copy   

•   Source: SciCrunch Registry

http://soybeangenome.siu.edu

It provides the mapping of relationships between soybean genomic features in a way that is presentable in GBrowse. It combines Perl MySQL database programming with Gbrowse to provide an integrated way of presenting soybean genomic features. The database is also searchable for listings of these relationships.

Proper citation: The Soybean GBrowse Database (RRID:SCR_013463) Copy   

•   Source: SciCrunch Registry

http://www.cstl.nist.gov/div831/strbase/

A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

Proper citation: STRBase (RRID:SCR_013465) Copy   

•   Source: SciCrunch Registry

http://www.nccc.com

Provides access to large scale cell culture at reasonable cost. The Cell Culture Center has experience with the production of over 1700 cell lines. Numerous common cell lines, such as HeLa, CHO, 293, BHK, and hybridomas are routinely produced at the Center. We will adapt your cell line or custom protocol to large scale production then deliver the cells in the quantity and frequency you need. Large Scale Production Services: Mammalian cells: Suspension culture (1 to 400 liters per day), Anchorage dependent culture (1 to 200 roller bottles per batch), Purified monoclonal antibodies (10 mg to 100 grams), Non-hybridoma cell secreted proteins, Conditioned media Secreted proteins from suspension cultures can be produced in automated hollow fiber bioreactor systems. These systems may be considered after initial static culture production yields are determined. Upon determining the quantities requested by the investigator, the appropriate automated system will be used. For more information on the automated instrumentation available for the use of secreted protein production, please refer to the Biovest International web page (www.biovest.com). Working with our experienced personnel and quality controlled, state-of-the-art facilities also permits access to large quantities of cells or protein so you aren''t limited by the cell culture capacities of your own laboratory. The Center fulfills the needs of small research laboratories as well as those of larger institutions. Customers from all sectors of the research and industrial community are welcome to inquire about our services. If you''d like to inquire about using our services, use the contact infromation below. Key words: Cell, cells, culture, monoclonal, antibodies, antibody.

Proper citation: National Cell Culture Center (RRID:SCR_013467) Copy   

•   Source: SciCrunch Registry

http://hbatlas.org

A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities.

Proper citation: Human Brain Transcriptome (RRID:SCR_013742) Copy   

•   Source: SciCrunch Registry