Resources

LungMAP:

LungMAP seeks to improve lung health by providing the research community with a comprehensive web-based atlas to support investigations into the processes that regulate lung development. The use of cutting-edge technologies will generate a novel map of where and when lung cells differentiate and alveoli form.

ENCODE: Encyclopedia of DNA Elements

The goal of ENCODE is to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active. The ENCODE Project has produced genome-wide data for over 100 different cell types for investigating different aspects of genomic regulation, including: chromatin structure (5C), open chromatin (DNase-seq and FAIRE-seq), histone modifications and DNA-binding of over 100 transcription factors (ChIP-seq) and RNA transcription (RNAseq and CAGE)

Primer Bank:

Primer Bank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. The primer design algorithm has been extensively tested by real-time PCR experiments for PCR specificity and efficiency.

:European Nucleotide Archive

The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation

 : DNA Data Bank of Japan

DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. 

LNCipedia.org: A comprehensive compendium of human long non-coding RNAs

Lncipedia.org is an integrated database of 111,685 human annotated lncRNA transcripts obtained from different sources. In addition to basic transcript information and structure, several statistics are calculated for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites.

Stealth RNAi™ Pre-Designed siRNAs

Now you can quickly and easily order Stealth RNAi™ siRNA - predesigned RNAi sequences to the majority of human, rat, and mouse genes. Stealth RNAi™ siRNA sequences are synthesized using the same advanced chemistry as all Stealth RNAi™ siRNA, and pre-designed in silico using the BLOCK-iT™ RNAi Designer. 

 : Protein Data Bank

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that help students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

 : Ensembl Mirror

The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

 : Influenza Reagent Resource

The Influenza Reagent Resource (IRR) was established by the Centers for Disease Control and Prevention (CDC) to provide registered users with reagents, tools and information for studying and detection of Influenza Virus. The IRR acquires, authenticates, and produces reagents that scientists need to carry out basic research and develop improved diagnostic tests, vaccines, and detection methods.

The ATCC Cell Biology Collection is one of the largest bioresources in the world, and offers a complex array of human, animal, insect, fish and stem cell lines from which to choose.

: BioLabs Inc.

NEB offers several helpful interactive tools for your research and experimental design. In addition, Double Digest Finder and Enzyme Finder are featured on NEBTools

DIANA -miRPath

DIANA-miRPath is a miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. miRPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions) provided by the DIANA-microT-CDS algorithm or even experimentally validated miRNA interactions derived from DIANA-TarBase v6.0. 

: miRBase: the microRNA database

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download.

: Target Scan Human - Prediction of microRNA Targets

TargetScan predicts biological targets of miRNAs by searching for the presence of 8mer, 7mer, and 6mer sites that match the seed region of each miRNA (Lewis et al., 2005). As an option, only conserved sites are predicted. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing (Friedman et al., 2009) and centered sites (Shin et al., 2010)

PROMO

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files

: DAVID Bioinformatics Resources

The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 is an update to the sixth version of our original web-accessible programs. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes

NONCODE - An integrated knowledge database dedicated to ncRNAs, especially lncRNAs.

Is an integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs. NONCODE tries to present the most complete collection and annotation of non-coding RNA. It not only provides the basic information of lncRNA such as location, strand, exon number, length and sequence, but also the advanced information such as the expression profile, conservation ,disease relation and the relative literature.

RNAcentral is a public resource that offers integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases. The development of RNAcentral is coordinated by European Bioinformatics Institute and is funded by BBSRC