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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.
Proper citation: PhenoDB (RRID:SCR_016551) Copy
Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.
Proper citation: Danish Twin Registry (RRID:SCR_017482) Copy
Database provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full studies or subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data.
Proper citation: Diversity Outbred Database (RRID:SCR_018180) Copy
https://hive.biochemistry.gwu.edu/dna.cgi?cmd=tissue_codon_usage&id=586358&mode=cocoputs
Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data.
Proper citation: Codon and Codon-Pair Usage Tables (RRID:SCR_018504) Copy
Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index.
Proper citation: Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) Copy
http://p300db.choudharylab.org
Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells.
Proper citation: p300db (RRID:SCR_017063) Copy
https://www.sdbonline.org/sites/fly/atlas/00atlas.htm
Collection of color illustrations that follow main events of embryogenesis and post embryonic development of Drosophila.
Proper citation: Atlas of Drosophila Development (RRID:SCR_017506) Copy
Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.
Proper citation: RegulomeDB (RRID:SCR_017905) Copy
Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.
Proper citation: CoMeTa Website (RRID:SCR_017357) Copy
http://mirtarbase.mbc.nctu.edu.tw/
Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.
Proper citation: miRTarBase (RRID:SCR_017355) Copy
Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain.
Proper citation: ABA Mouse Brain: Atlas (RRID:SCR_017479) Copy
http://www.broadinstitute.org/pubs/MitoCarta/
Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.
Proper citation: MitoCarta (RRID:SCR_018165) Copy
http://geno2mp.gs.washington.edu/Geno2MP/#/
Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.
Proper citation: Geno2MP (RRID:SCR_016872) Copy
Database of intracellular recordings of non-human primates (NHP) cells sampled from the lateral prefrontal cortex. 249 patch clamp recordings for 2 protocols: 1 second current pulse and 3 millisecond pulse. Morphology obtained by biocytin injections and confocal imaging at 63x magnification.
Proper citation: Primate Cell Type Database (RRID:SCR_017963) Copy
https://bioinformatics.niaid.nih.gov/chemokinedb/
Resource of chemokines and receptors with detailed information including taxonomy, nomenclature, structure, physiological function, tissue information, and phenotype, collected from IUPHAR/BPS, UniGene, and UniProt public databases.
Proper citation: ChemokineDB (RRID:SCR_016593) Copy
Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system.
Proper citation: mousebrain.org (RRID:SCR_016999) Copy
Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class.
Proper citation: ResistomeDB (RRID:SCR_018305) Copy
Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases.
Proper citation: GEROprotectors (RRID:SCR_016737) Copy
http://meme-suite.org/tools/dreme
Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences).
Proper citation: DREME (RRID:SCR_016860) Copy
https://pregnancycolab.tghn.org/collect/
Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required.
Proper citation: COLLECT database (RRID:SCR_018366) Copy
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