National Centers for Systems Biology
Research Services & Instrumentation
Back to topCenter for Complex Biological Systems (UC Irvine)
The Laboratory for Fluorescence Dynamics (LFD) is a national research resource center for biomedical fluorescence spectroscopy, supported by the National Center for Research Resources division of the National Institutes of Health (grant number PHS 5 P41-RR003155), and the University of California, Irvine. The founder and Principal Investigator of the LFD is Enrico Gratton. The LFD’s main activities are:
- Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists.
- Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications.
- Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.
Center for Modular Biology (Harvard University)
Harvard core facility
The core facilities at the Harvard Center for Modular Biology provide state-of-the-art instrumentation and expertise in genomic technologies, automation and bioinformatics to scientists at Harvard and outside. Our technical staff provide expertise and hands-on training in protocols and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.
Center for Quantitative Biology (Princeton University)
Lewis-Sigler Institute Microarray Facility
The Microarray core facility is fully equipped for all aspects of microarray production and data acquisition. Complementary DNA, (cDNA’s) and PCR products are amplified and quality checked using the high throughput liquid handling Beckman Coulter Biomek FX, and MJ Research Tetrad thermocyclers. Spotting of PCR products or long Oligomers is accomplished on in-house Arrayers built according to the Joe DeRisi, Pat Brown design and operated by software written by Joe DeRisi. Hybridization probes are checked prior to labeling using the Agilent Bioanalyzer 2100 and the Nanodrop spectrophotometer. Post labeling efficiency is quantified by Nanodrop prior to application of probes to the array. Post-hybridization image acquisition is accomplished using any of two available scanners, an Axon 4200A Professional Scanner equipped with four laser scanning capability, or an Agilent Microarray scanner , two color, equipped with a 48 slide auto-sampler carousel. Data extraction from the images is accomplished using Axon’s Genepix software, versions 4.0, 5.1, or 6.0, or Agilent’s data feature extraction software v 9.5. The facility also offers access to an Affymetrix Array station consisting of two fluidics stations handling four chips each, a hybridization oven, and a scanner-3000 complete with the “7G” upgrade. GCOS software is available for data analysis. Two computer workstations are available with Acuity 4.0 Software, and one with Pathway Assist Software. Complementary to microarray analysis the facility offers access to two ABI 7900 quantitative PCR machines, one equipped with a 96 well block, the other with a 384 well block and robotic plate loader. The facility also offers next generation sequencing services using the Illumina Genome Analyzer IIX, and offers custom data analysis consulting. The entire lab space is ozone free protecting dye integrity of samples. Personnel are available to contract for any and all aspects above, or to train, assist and troubleshoot..
Lewis-Sigler Institute Imaging Facility
The increasing need for quantitative optical methods in biology often requires specialized instrumentation. The Imaging Core Facility was created with the idea of offering researchers at the University a set of instruments that can be tailored to their particular application as well as help in implementing the set-up the most appropriate. The facility opened in March 2006, and now has three two-photon scanning microscopes available. The hardware and the control software for all three instruments are flexible enough to permit modifications for specific experiments. Researchers can book the instruments for extended periods of time (up to several weeks in a row if necessary).
Princeton Mass Spectrometry and Synthesizing / Sequencing Facility
The Mass Spectrometry Facility is one of the centralized service facilities of the Molecular Biology Department at Princeton University. Our primary goal is to provide state-of-the-art analytical services to researchers who demand sophisticated modern instrumentation in the area of nucleic acid and protein chemistry.
Center for Systems Biology (Institute for Systems Biology)
Innovative research consistently drives the development of new technologies to explore new areas of data space. The Center core facilities encompass major systems biology technologies; proteomics, genomics, informatics, microfluidics and imaging and has a major focus on developing standard operating procedures and data standards. The Center focuses its resources to enable systems biology through the cores in three fundamental ways. In cases where technologies are mature (for example microarrays), the Center provides access for all Center scientists (democratizing access). The Center also provides opportunities to drive the development of new technologies that enable projects within the Center (e.g. comprehensive phosphoproteomics and single-cell analyses). Between these extremes lies the majority of state of the art technologies. In these cases, the proof of principle is established, but the technologies remain insufficiently robust for wide dissemination. The Center provides access to these early stage technologies (e.g. microfluidics and informatics). Sample preparation, data standardization and quality control are primary foci for the Center core facilities.
Genomics. Recent advances in genomics technologies, primarily in high-throughput, short read, cyclic array sequencing platforms such as the Illumina Genome Analyzer and the Applied Biosystems SOLiD have had major impacts on the genomics core facility. We have implemented these technologies (among others) to improve throughput (through multiplexing) and sensitivity, and to reduce cost. The challenge for the Core has been in analysis of the data. Thus, driven by collaborations with Center research projects, the Core has established pipelines for using these instruments for resequencing, gene expression (RNAseq) and DNA-protein interactions. In continued efforts to increase sensitivity and throughput of RNA measurements to the single-molecule and single-cell levels, the Core has also established the NanoString Technology nCounter platform (85)and a multiplexed microfluidic platform (Fluidigm Biomark) for RT-PCR (86).
Proteomics. Collaborations between the proteomics core and researchers of the Center have facilitated the development of numerous advances, leading to increased sensitivity, increased sample coverage, and increased detection and quantification of post-translational modifications and complexes. Advances in proteomics have occurred at the level of instruments, sample preparations, and computational proteomics. Most excitingly, targeted mass spectrometry techniques (e.g., SRM) can now target individual species in a high throughput manner, avoiding the sampling pitfalls of standard shotgun approaches. The center has also helped catalyze the development of the computational software necessary for targeted proteomics as well as the trans proteomic pipeline (to interpret MS data) and the peptide atlas (a database for validated protein mass spectra).
ICM Core. The Imaging Cytometry and Microfluidics Core was established by the Center to extend high throughput ‘omics based measurements to multiparameter high throughput quantitative imaging. In collaboration with Center research programs, the ICM core has developed and/or implemented state of the art capabilities in microscopy, cytometry and microfluidics. These multiparameter phenotype measures are critical to the advancement of systems biology because they enable dynamic data acquisition and analyses ranging from the subcellular to multicellular scales and multiplexed exquisitely controlled environments and perturbations in a microfluidics environment for multiscale modeling – a focus of this renewal. In recognition of these needs in the systems biology community, the Center also established a course on imaging and microfluidics run by the ICM core.
Informatics. In recognition of the central role for informatics in systems biology, the Center funded the development of the informatics core in 2006. The core collaborates with all of the facilities and research groups across the ISB. The core also collaborates and co-develops software with a number of groups outside of the ISB. The informatics core provides tools and analysis pipelines, software infrastructure and standards to all research projects. The core has authored publications with a number of these groups, and has also been jointly awarded research grants. The core also continually evaluates new technologies and tools, and recommends their usage to the different groups where appropriate. This evaluation extends to both new software and hardware. All software developed by the core is made freely available to all. Source code, with artifact management, is provided. Primarily, dissemination of computational research outside of ISB occurs through publications. Dissemination of informatics tools and data outside of ISB is primarily through our external collaborations, training, and the website.
Back to topChicago Center for Systems Biology
BAC-Recombineering Core (BRC)
The BAC-Recombineering Core can provide investigators affiliated with CBC schools the capability to dynamically image fluorescently tagged proteins in model organisms and measure spatiotemporal expression of protein of interest.
The IGSB Cellular Screening Center (CSC)
CSC houses a state-of-the art high throughput cellular screening facility which opened in 2007. Support from the Chicago Biomedical Consortium and The University of Chicago Biological Sciences Division enabled the creation of the CSC. The CSC facilitates drug discovery and development by defining the complex genetics underlying disease, isolating chemical compounds that affect specific cellular activities, and developing potential therapeutics to target disease pathways. Automation is present for all aspects of the screening process. Without automation a 300 plate screen would take as long as 2 months. With the automation present in the CSC the same screen can be performed in as little as 2 days. CSC facilities are available to a broad network of Chicago area investigators on a collaborative basis established through internal and external funding. The Center has attracted a significant number of collaborations with area scientists in fields as diverse as cancer biology, diabetes and ophthalmology.
The IGSB High-Throughput Genome Analysis Core (HGAC)
HGAC is a state-of-the-art facility providing resources and services for ultra-high-throughput sequencing and large-scale microarray processing. Operated by the Institute for Genomics and Systems Biology, the HGAC facility is available to University of Chicago and Argonne National Laboratory investigators and their collaborators
Micro-Western Array Core (MWA)
The Micro-Western Array (MWA) Core is a technological initiative designed to provide a quantitative platform for studies of abundance and modification of pre-selected protein targets.
New Mexico Center for Spatiotemporal Modeling of Cell Signaling
Institutional Core Facilities
STMC scientists led the development of excellent institutional core facilities for Electron Microscopy, Flow Cytometry and Fluorescence Microscopy. The resources offered in these mature cores are described at:
Electron Microscopy
Flow Cytometry
Fluorescence Microscopy
STMC Technology
STMC scientists continue to develop new electron microscopy and fluorescence-based imaging technologies for cell signaling research.
San Diego Center for Systems Biology (UC San Diego)
SDCSB’s three core facilities
Systems Biology takes advantage of emerging interdisciplinary technologies and approaches. As such core facilities specializing in specific cutting edge technologies that can be applied to many biological questions play an important role in Systems Biology research. Our three Cores main function is to help promote the development and to facilitate the adoption of important Systems Biology approaches. Specifics for each Core and how to utilize the resources are available at:
SDCSB Network Bioinformatics Core
SDCSB Mathematical Modeling Core
SDCSB Cell Dynamics Core