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http://www.bumc.bu.edu/busm-pathology/pathology-core-services/biospecimen-archive-research-core-barc/

Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org

Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy   

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http://www.youtube.com/user/WholeBrainCatalog?feature=autoshare

Videos uploaded to YouTube by the Whole Brain Catalog.

Proper citation: WholeBrainCatalog's Channel - YouTube (RRID:SCR_005436) Copy   

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http://highwire.stanford.edu/

Service that partners with independent scholarly publishers, societies, associations, and university presses to facilitate the digital dissemination of 1779 journals, reference works, books, and proceedings. It also offers a complete manuscript submission, tracking, peer review, and publishing system for journal editors.

Proper citation: HighWire (RRID:SCR_005316) Copy   

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http://med.emory.edu/ADRC/research/core_neurology_database.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9, 2025. A database which retains extensive clinical information about study subjects recruited by the Alzheimer's Disease Research Center Clinical Core, as well as other individuals with neurological diseases. In addition to clinical information, the database has basic demographics, medical history (including risk factors such as smoking), and a detailed family history from all subjects. Some entries have neuropsychological measures. Users can access a Summary Database which contains the most commonly requested variables. A data dictionary describing the variables in the Summary Database is available.

Proper citation: Emory Neurology Database (RRID:SCR_005277) Copy   

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http://maize.tigr.org

A database of maize genomic sequences, searchable by BLAST, by repeat sequences, and sequence name, gene name, locus, or other landmark. TIGR is a member of the Consortium for Maize Genomics. The Consortium received a funding award from the National Science Foundation in September 2002, to evaluate two gene-enrichment techniques, methylation filtration and high Cot selection, to sequence the maize 'genespace'. Draft assemblies of 287 maize BAC clones selected by the maize community and the Consortium were also produced in the Consortium project. We have recently developed an improved version of the TIGR annotation pipeline optimized for maize genomic assemblies. The latest maize genomic assemblies obtained by gene-enrichment (AZM5) and the 287 maize draft BAC assemblies have been annotated using the improved pipeline. Gene model annotation and functional annotation can be accessed via the TIGR maize BLAST server or the TIGR maize gbrowse display. The first version of the Maize Repeat Database contained 485 characterized maize repeat sequences from the TIGR Cereal Repeat Database. To these we added repetitive sequences downloaded from GenBank and a file of retrotransposon sequences compiled by Phillip SanMiguel (Purdue University). In addition we searched our maize genomic assemblies (AZMs) to identify new repeats. Any sequence within an AZM that showed at least 80% identity over a minimum stretch of 100 bp with an entry in the TIGR Cereal Repeat Database was coded accordingly and added to the Maize Repeat Database.

Proper citation: TIGR Maize database (RRID:SCR_005431) Copy   

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http://cmrm.med.jhmi.edu/cmrm/atlas/human_data/file/JHUtemplate_newuser.html

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

Proper citation: DTI White Matter Atlas (RRID:SCR_005279) Copy   

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http://med.brown.edu/neurology/brainbank/index.html

A tissue resource center which facilitates research into the relationship between Alzheimer's disease and other brain disorders such as strokes and mental illnesses. Most donations have been obtained from Alzheimer's patients. Normal controls are available, many of which are from subjects with close relatives with Alzheimer's. The Brown BTRC also supports a collection of brain tumor cases that were harvested from patients who underwent surgery and who were enrolled in a clinical trial for the development of new treatments for brain cancer.

Proper citation: Brown Brain Tissue Resource Center (RRID:SCR_005392) Copy   

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http://rnp.uthscsa.edu/rnp/tmRDB/tmRDB.html

The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called 10S RNA). As the name implies, tmRNA has properties of tRNA and mRNA combined in a single molecule. The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, we established direct links to primary sources. We acknowledge support provided by the National Institutes of Health and the Danish Technical Research Council. tRNA, mRNA, trans-translation, rescue, ribosome, broken mRNA, bacteria, mitochondria chloroplasts, cyanelles, bacteriphage, phylogenetic

Proper citation: tmRNA Database (RRID:SCR_005540) Copy   

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http://tmbeta-genome.cbrc.jp/annotation/

A collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. TMBETA-GENOME has the feasibility of selecting the organism from the three kingdoms of life, archaea, bacteria and eukaryote. Further, users have the option to select any of the methods or their combinations, and display the results with/without amino acid sequence information.

Proper citation: TMBETA-GENOME- Annotation of Beta-Barrel Membrane Proteins in Genomic Sequences (RRID:SCR_005538) Copy   

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http://www.biosino.org/bodyfluid/

A database of bodily fluid proteome data. It contains information on proteins from humanplasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Our body fluid protein database, Sys-BodyFluid, contains 11 body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid. Over 10,000 proteins are included in the Sys-BodyFluid. These body fluid proteome data come from 50 peer-review publications of different laboratories all over the world. Protein annotation are provided including protein description, Gene ontology, Domain information, Protein sequence and involved pathway. User can access the proteome data by protein name, protein accession number, sequence similarity. In addition, user could perform query cross different body fluids to get more comprehensive understanding. The difference and similarity between these 11 body fluids are also analyzed. Thus , the Sys-BodyFluid database could serve as a reference database for body fluid research and disease proteomics. plasm, serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk, and amniotic fluid, protein, proteomics

Proper citation: Sys-BodyFluid (RRID:SCR_005335) Copy   

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http://www.labspaces.net/DNA

Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

Proper citation: Daring Nucleic Adventures - genegeek (RRID:SCR_005215) Copy   

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http://www.knockoutmouse.org/

Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs.

Proper citation: International Knockout Mouse Consortium (RRID:SCR_005574) Copy   

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http://swissregulon.unibas.ch/fcgi/sr/swissregulon

A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format.

Proper citation: SwissRegulon (RRID:SCR_005333) Copy   

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http://www.einstein.yu.edu/centers/ictr/

Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research.

Proper citation: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository (RRID:SCR_005297) Copy   

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http://wishart.biology.ualberta.ca/polysearch/index.htm

A web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.

Proper citation: PolySearch (RRID:SCR_005291) Copy   

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http://www.jax.org/grc/index.html

Donate a strain to The Jackson Laboratory Repository. Why donate a strain? * Donating reduces your costs of maintaining strains, lab personnel, shipping and resources. * Each donated strain is cryopreserved, protecting against accidental loss and genetic contamination. * Each donated strain is rederived to a high health status and may be resupplied to donors (up to 3 breeder pairs as long as we have live mice available) * Donating fulfills NIH obligations to share mice. How strain donation works: Strains are submitted by investigators for distribution to the scientific community. All repository strains are cryopreserved. All strains are evaluated monthly by the Genetic Resource Committee (GRC). The GRC is made up of staff scientists and resource managers from The Jackson Laboratory. The GRC recommends which strains are most appropriate to include in the Repository. You will be notified by email after your strain has been reviewed. Donation evaluation criteria * Importance of its current use for research, publication history, and current demand * Importance of its anticipated or potential future use * Difficulty of maintenance relative to scientific value * Existence and reliability of other resources that would ensure its survival * Difficulty of re-creating the strain relative to the time and effort required for its importation and preservation

Proper citation: Donate a strain to The Jackson Laboratory Repository (RRID:SCR_005567) Copy   

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http://katahdin.mssm.edu/kismeth/revpage.pl

A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species.

Proper citation: Kismeth (RRID:SCR_005444) Copy   

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http://ssd.rbvi.ucsf.edu/

The SSD has been developed to address the need for resources and tools for understanding large sets of superpositions in order to understand evolutionary relationships and to make predictions of function. We have therefore created the Structure Superposition Database (SSD) for accessing, viewing and understanding large sets of structure superposition data. It contains the results of pairwise, all-by-all superpositions of a representative set of 115 (beta/alpha) barrel structures (TIM barrels). The initial implementation of the SSD contains the results of pairwise, all-by-all superpositions of a representative set of 115 (/alpha)8 barrel structures (TIM barrels). Future plans call for extending the database to include representative structure superpositions for many additional folds. The SSD can be browsed with a user interface module developed as an extension to Chimera, an extensible molecular modeling program. Features of the user interface module facilitate viewing multiple superpositions together.

Proper citation: Structure Superposition Database (RRID:SCR_005236) Copy   

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http://neurosphere.wordpress.com/

This blog belongs to me, Dave J Hayes PhD, a Neuroscientist at the University of Ottawa''s Institute of Mental Health Research. My research focuses on the neuroscience of motivation and emotion particularly regarding how brains and people respond to aversive and rewarding things in their environment. A neurosphere is a free-floating group of neural stem cells which can multiply, outside of their natural environment, and retain the ability to differentiate into functional brain cells. I don''t work on neurospheres. However, i like the metaphor of a group of people coming together, outside of their natural environment, through their interest in all things neuro which, incidentally, is everything. The sphere of human thought.

Proper citation: neurosphere (RRID:SCR_005478) Copy   

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http://transpogene.tau.ac.il/

A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome.

Proper citation: TranspoGene (RRID:SCR_005634) Copy   

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