Genomics Proteomics Core
The Genomics and Proteomics Core at BIDMC provides all the tools of modern functional genomics and proteomics for academic and corporate clients alike, including state-of-the-art technologies for
- Transcriptional profiling
We have recently added the exciting and powerful new, cutting edge proteomics assay, SOMAscan, from SomaLogic. The core is the exclusive service provider for this 1310 protein biomarker discovery platform in the Boston/Longwood Medical Area.
SOMAscan (SomaLogic) is a high multiplex, high sensitivity aptamer-based immune-like protein and biomarker discovery platform that simultaneously quantifies 1,310 human proteins in all types of protein extracts from bodily fluids such as serum, plasma, urine, saliva, CSF, cyst fluid, and tissue, cells, lavage, animal models and exosomes.
The Genomics Core offers Affymetrix gene chip technologies, both cartridge based and 96 well high throughput. We have protocols to analyze genomic information with as little as 50ng of RNA, RNA extracted from paraffin based samples, or even partially degraded RNA.
- GeneChip HT Genome Array Plate Set - New GeneChip HT System designed to complete large projects of up to 96 samples per run, including human, mouse and rat
- Whole Genome Cartridge Gene Arrays
- We offer amplification services for limited amount of RNA and partially degraded RNA (FFPE)
The Proteomics Core will provide a comprehensive array of services pertaining to the design, performance and analysis of proteomic studies. The core not only offers the ability to implement and validate previously developed proteomic methods to profile proteins in biological fluids and tissues, to quantitate proteins, to identify proteins and their posttranslational modifications, and to study protein-protein interactions, but also the capability to modify or develop entirely new assays when warranted.
- High multiplex, high sensitivity aptamer-based SOMAscan-1310 protein biomarker discovery
- Relative quantitation by µLC/MS/MS
- ITRAQ - 8-plex isobaric peptide tagging system that enables you to label all primary amines, regardless of peptide class
- SILAC - stable isotope labeling of amino acids in cell culture which is a biosynthetic approach
- GIST - global internal standard technology, a post digestion peptide level labeling technique
- ICAT - isotope coded affinity tag -based protein profiling
- Protein identification by LC-MALDI and LC/MS/MS
- Coomassie & silver stained gel band
- Identification of protein and peptide modifications
- Phosphorylation sites
- Protein modifications such as acetylation, methylation, and ubiquitination
- Coomassie stain only, purified proteins
- Protein profiling of complex biological samples (serum, urine, CSF, biopsies tissue, cell extracts, lavage, saliva, etc).
- Profiling by µLC/MS
- Multidimensional protein fractionation by µLC
Data Analysis and Bioinformatics Services
In addition, the core offers a full bioinformatics core for data management and analysis as well as new software development and the capability to perform a wide variety of genomic and high throughput assays.
The Bioinformatics Core will provide investigators with access to phenotypically annotated proteomics data as well as a large set of analytic procedures (i.e. unsupervised and supervised learning techniques, statistical analysis tools, automated clustering and classification procedures, pathway analysis and generation tools, protein identification database tools, data-visualization tools, annotation tools) with which to explore the data sets for further hypothesis generation.