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Found 39 result(s)

Stanford Microarray Database

SMD

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>>>!!!<<< SMD has been retired. After approximately fifteen years of microarray-centric research service, the Stanford Microarray Database has been retired. We apologize for any inconvenience; please read below for possible resolutions to your queries. If you are looking for any raw data that was directly linked to SMD from a manuscript, please search one of the public repositories. NCBI Gene Expression Omnibus EBI ArrayExpress All published data were previously communicated to one (or both) of the public repositories. Alternatively, data for publications between 1997 and 2004 were likely migrated to the Princeton University MicroArray Database, and are accessible there. If you are looking for a manuscript supplement (i.e. from a domain other than smd.stanford.edu), perhaps try searching the Internet Archive: Wayback Machine https://archive.org/web/ . >>>!!!<<< The Stanford Microarray Database (SMD) is a DNA microarray research database that provides a large amount of data for public use.

Expressed Sequence Tags database

dbEST

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dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

ENCODE

Encyclopedia of DNA Elements

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The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

JASPAR

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JASPAR is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors and other proteins interacting with DNA in a sequence-specific manner.

Greengenes

The Greengenes Database

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Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

PeptideAtlas

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The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.

ChIP-Seq Transcription Factor Data

ChIP-Seq

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We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.

CIS-BP

Catalog of Inferred Sequence Binding Preferences

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The Catalog of Inferred Sequence Binding Preferences (CIS-BP) is a library of transcription factor (TF) DNA binding motifs and specificities. The data are organized in a user friendly manner for ease of searching, browsing, and downloading. CIS-BP also includes built-in web tools for scanning DNA sequences for putative TF binding sites, predicting the DNA binding motif of a given TF, and identifying a TF that might recognize a given DNA motif.

MUCL Agro-food & Environmental Fungal Collection

BCCM/MUCL Agro-food & Environmental Fungal Collection

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BCCM/MUCL is a generalist fungal culture collection of over 30000 filamentous fungi, yeasts and arbuscular mycorrhizal fungi including type, reference and test strains. It provides curated documentation and information on these bioresourced in its database. The collections activities include the distribution of its holdings, the accession of new material in its public, safe and patent domains, and services valorising its holdings and/or expertise to cultivate, isolate and identify fungal diversity in natural and anthropological ecosystems, agro-food (food and feed transformation and spoilage), and fungal-plant interactions.

European Xenopus Resource Center

EXRC

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The European Xenopus Resource Centre (EXRC) is situated in Portsmouth, United Kingdom and provides tools and services to support researchers using Xenopus models. The EXRC depends on researchers to obtain and deposit Xenopus transgenic and mutant lines, Xenopus in-situ hybridization clones, Xenopus specific antibodies and other resources with the centre. EXRC staff perform quality assurance testing on these reagents and then makes them available to the community at cost. EXRC also supplies wild type Xenopus, embryos, oocytes, egg extracts, X.tropicalis Fosmids, X.laevis BACs and ORFeomes.

cisRED

Databases of genome-wide regulatory module and element predictions

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Genome Sequence Archive

GSA

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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

dictybase

Dictyostelium discoideum

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dictyBase is an integrated genetic and literature database that contains published Dictyostelium discoideum literature, genes, expressed sequence tags (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct access to the genome browser, a Blast search tool, the Dictyostelium Stock Center, research tools, colleague databases, and much much more are just a mouse click away. Dictybase is a genome portal for the Amoebozoa. dictyBase is funded by a grant from the National Institute for General Medical Sciences.

UniGene

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<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the “UniGene Cluster Number” field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.

Conservation Genome Resource Bank for Korean Wildlife

CGRB

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Genome resource samples of wild animals, particularly those of endangered mammalian and avian species, are very difficult to collect. In Korea, many of these animals such as tigers, leopards, bears, wolves, foxes, gorals, and river otters, are either already extinct, long before the Korean biologists had the opportunity to study them, or are near extinction. Therefore, proposal for a systematic collection and preservation of genetic samples of these precious animals was adopted by Korea Science & Engineering Foundation (KOSEF). As an outcome, Conservation Genome Resource Bank for Korean Wildlife (CGRB; www.cgrb.org) was established in 2002 at the College of Veterinary Medicine, Seoul National University as one of the Special Research Materials Bank supported by the Scientific and Research Infrastructure Building Program of KOSEF. CGRB operates in collaboration with Seoul Grand Park Zoo managed by Seoul Metropolitan Government, and has offices and laboratories at both Seoul National University and Seoul Grand Park, where duplicate samples are maintained, thereby assuring a long-term, safe preservation of the samples. Thus, CGRB is the first example of the collaborative scientific infrastructure program between university and zoo in Korea.

Addgene

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Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

modENCODE

Model Organism ENCyclopedia of DNA Elements

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<<<!!!<<< As of 2023, support to maintain the www.modencode.org and intermine.modencode.org sites have been retired following the end of funding. To access data from the modENCODE project, or for questions regarding the data they make available, please visit these databases: Fly data: FlyBase: ModENCODE data at FlyBase: https://wiki.flybase.org/wiki/FlyBase:ModENCODE_data_at_FlyBase FlyBase: https://www.re3data.org/repository/r3d100010591 Worm data: WormBase https://www.re3data.org/repository/r3d100010424 Data, including modENCODE and modERN project data, is also available at the ENCODE Portal: https://www.re3data.org/repository/r3d100013051 (search metadata and view datasets for Drosophila and Caenorhabditis https://www.encodeproject.org/matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.donor.organism.scientific_name=Drosophila+melanogaster&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis+elegans&replicates.library.biosample.donor.organism.scientific_name=Drosophila+pseudoobscura&replicates.library.biosample.donor.organism.scientific_name=Drosophila+mojavensis). >>>!!!>>>

MicrosporidiaDB

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MicrosporidiaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the phylum Microsporidia. In its first iteration (released in early 2010), MicrosporidiaDB contains the genomes of two Encephalitozoon species (see below). MicrosporidiaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.

CryptoDB

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CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium and other related genera. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.

Atlas of Living Australia

ALA

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The Atlas of Living Australia (ALA) combines and provides scientifically collected data from a wide range of sources such as museums, herbaria, community groups, government departments, individuals and universities. Data records consist of images, literature, molecular DNA data, identification keys, species interaction data, species profile data, nomenclature, source data, conservation indicators, and spatial data.

DNA Data Bank of Japan

DDBJ

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DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

GallusReactome

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>>>!!!<<< 29.01.2020: Gallus.Reactome is offline >>>!!!<<<

Sequence Read Archive

SRA

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The Sequence Read Archive stores the raw sequencing data from such sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer, the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq, Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.