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Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.
Proper citation: Eukaryotic Promoter Database (RRID:SCR_002132) Copy
http://caps.ncbs.res.in/stifdb2/
Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.
Proper citation: STIFDB (RRID:SCR_002131) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.
Proper citation: Transcription Factor encyclopedia (RRID:SCR_002130) Copy
http://megasun.bch.umontreal.ca/ogmpproj.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.
Proper citation: Organelle Genomics (RRID:SCR_002137) Copy
Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.
Proper citation: WikiPathways (RRID:SCR_002134) Copy
https://omictools.com/protein-interactions-and-molecular-information-database-tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible.
Proper citation: Protein interaction and molecular information database (RRID:SCR_002096) Copy
http://pathway.gramene.org/gramene/ricecyc.shtml
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.
Proper citation: Rice Metabolic Pathway Database (RRID:SCR_002128) Copy
A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.
Proper citation: pSTIING (RRID:SCR_002045) Copy
http://www.speciation.net/Database/Instruments/Carl-Zeiss-AG/LIBRA-120-;i672
Electron microscope by Carl Zeiss AG which combines flexibility and ease of use of new control electronics, Windows® based user interface and a vacuum system.
Proper citation: Zeiss: libra 120 transmission electron microscope (RRID:SCR_016703) Copy
Instrument provides acquisition of up to 12 parameters with optical design for enhanced sensitivity for multicolor assays. With customized forward scatter, to achieve accurate size measurement, and optimized electronics for high resolution and fast, accurate processing for researchers needs.
Proper citation: Gallios: Flow Cytometer (RRID:SCR_016702) Copy
https://www.neuronexus.com/files/catalog/NeuroNexus-2023ProbeDesignCatalog.pdf
Instrument as a 16 channel linear electrode array from NeuroNexus Technologies, Ann Arbor, Michigan. Used to map brain function, detect neural activity, and stimulate or modulate neural circuits when brain function is impaired. Used for small and large animal models for neuroscience and clinical applications.
Proper citation: Neuronexus: Neural Probe A1x16-3mm-100-703 (RRID:SCR_016678) Copy
https://www.a-msystems.com/p-285-model-2100-isolated-pulse-stimulator.aspx
Instrument used for a variety of physiological stimulation protocols, including behavioral feedback, LTP/LTD, lesion making, electrode marking, ultrafast timing applications, orthodromic/antidromic stimulation, and kindling. Used in a neurophysiological and physiological experiment protocols.
Proper citation: A-M SYSTEMS: Model 2100 Isolated Pulse Stimulator (RRID:SCR_016677) Copy
https://www.colinst.com/oxymax-clams
Instrumentation for monitoring behavior and physiology in lab animals by Columbus Instruments. Used for simultaneous multi parameter assessment of 1 to 32 test animals with automated operation for experiments lasting up to three days.
Proper citation: Columbus Instruments: Oxymax-CLAMS (RRID:SCR_016718) Copy
Instrument for cell sorting by BD Biosciences where positive air pressure forces sample cell through an optically gel-coupled cuvette . Hydrodynamic focusing guides particles in a single-file stream through the cuvette, where laser light intercepts the stream at the sample interrogation point.Fluorescence activated cell sorting instrument. Flow cytometer as high speed fixed alignment benchtop cell sorter. Enables multicolor analysis of up to 13 fluorescent markers and two scatter parameters at time.
Proper citation: BD Biosciences: FACSAria III Cell Sorter (RRID:SCR_016695) Copy
Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: dCAS (RRID:SCR_016612) Copy
https://www.apple.com/numbers/
Software tool to create spreadsheets that include tables and images. You can use Apple Pencil on your iPad to add diagrams and colorful illustrations.
Proper citation: Numbers (RRID:SCR_016950) Copy
https://github.com/tarokiritani/WhiskerTracking
ImageJ plugins and macros for whisker tracking. Set of Fiji plugins and macros for tracking a single whisker.
Proper citation: Whisker tracking macro (RRID:SCR_016953) Copy
https://affinity.serif.com/en-us/photo/
Software tool for professional photo editing.
Proper citation: Affinity Photo (RRID:SCR_016951) Copy
https://www.olympus-global.com/technology/museum/micro/2004/
FV1000 confocal laser scanning biological microscope features twin scan system which enables spectroscopy of living intercellular contents and analysis of objects down to a 2nm wavelength resolution. Image size is increased to 4096x4096 pixels.
Proper citation: Olympus: FV1000 Confocal Microscope (RRID:SCR_016840) Copy
https://www.leicabiosystems.com/us/histology-equipment/cryostats/leica-cm3050-s/
Instrument designed for cryosectioning in biomedical, neuro-anatomical and pharmaceutical research.
Proper citation: Leica: CM3050 S Research Cryostat (RRID:SCR_016844) Copy
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