UMMS RNAi Core Facility UMMS has purchased the complete collections of human and mouse retroviral and lentiviral short hairpin RNA (shRNA) libraries from Open Biosystems, and has negotiated with them to distribute clones to UMass researchers (Amherst, Boston, Dartmouth, Lowell and Worcester campuses ONLY) at a reduced price
Bioinformatics Core A team of bioinformatics analysts and software engineers dedicated to providing comprehensive bioinformatics and computational infrastructure support for the biomedical research at UMMS.
Clinical Informatics Provides support for the conduct, administration, analyses, and dissemination of clinical and translational research from bench to clinic to populations.
Proteomics and Mass Spectrometry Facility Offering state-of-the-art proteomic and small molecule mass spectrometric analyses from study and design, sample preparation, protein fractionation, instrumentation, informatics, and data interpretation.
Small Molecule Screening Assists researchers in developing high-throughput (HT) screening assays, performs HT screens of chemical libraries to identify new small molecules to probe biological processes of interest.
Transgenic Animal Modeling Core To produce genetically-altered mice for the UMASS Medical School Community. The Core has generated more than 300 different lines of transgenic mice, targeted over 60 genes in mouse ES cells, produced over 120 lines of gene-targeted mice via blastocyst injection, and has cryopreserved over 100 lines of mice.
Entrez Programming Utilities (eUtils) Tools that provide access to Entrez data outside of the regular web query interface also helpful for retrieving search results for future use in another environment. Note: to submit large queries to the NCBI data base download in batch mode.
Perl Tutorial assumes a very basic knowledge of UNIX and concentrates on how to write basic working perl programs.
Sequence Read Archive (SRA) Stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helico , Heliscope, and others.
UCSB Genome Browser The reference sequence and working draft assemblies for a large collection of genomes. Also a portal to the ENCODE project.
miRBase Searchable database of published miRNA sequences and annotation.
The Exelixis Collection Generated by Exelixis Inc. and donated to Harvard Medical School to be distributed to the academic research community.
KYOTO Stock Center (DGRC) Drosophila Genetic Resource Center, in KYOTO Japan, collects, maintains and supplies genetic stocks Drosophila melanogaster to Drosophila researchers worldwide.
Vienna Drosophila RNAi Center (VDRC) Maintains and distributes transgenic RNAi stocks constructed by Dickson and Keleman groups at the IMP. GD and KK collections covering a total 13,264 Drosophila genes.
Nucleic Acid Folding
RNAfold Will predict secondary structures of single stranded RNA or DNA sequences.
RNAhybrid For finding the minimum free energy hybridization of two RNA's.
SFold Software for Statistical Folding and Rational Design of Nucleic Acids.
The RNAi Web A resource center for RNA interference (RNAi) technology.
RNAxs A site to design potent siRNAs to knock down your gene(s) of interest. Includes all the parameters that have been shown to influence RNAi efficiency in literature.