About Core Instrumentation Facility
Core Instrumentation Facility (CIF) of UCR Institute for Integrative Genome Biology
supports the campus research enterprise with tools for handling genomic
and cDNA libraries including robotic handling of colony picking,
extraction and purification of plasmids from bacterial cultures in microtiter
plates, handling of liquids for setting up PCR reactions and purification of
products for DNA sequencing. For genotyping
we offer sizing of amplified microsatellites and training in use of computer
software for analyzing fragment data. For gene expression studies
we have services and instrumentation for processing RNAs associated with use of
commercial GeneChips® from Affymetrix, robotic production of spotted
microarrays and scanning after hybridization, and analysis including gene-chip
image processing and data mining. For validation in gene expression studies we
offer quantitative PCR. In image analysis we
offer training in and use of a fluorescence imager/phosphorimager. For fluorescence
cytometric and sorting applications with whole cells, we offer
services employing our advanced cell sorter, the BD FACSAria. Protein chemistry
services including N-terminal protein sequencing and peptide synthesis
capabilities have been discontinued except in special cases. See
"Services" link at left for an overview of our services and the links
at the top of the page for details about specific services.
Instrumentation
Genomics
· Genetix QPIX for automated colony picking and macroarray making. Conventional size culture plates or large plates up to can be up to 22 cm square can be used for picking. Macroarray printing onto nylon membrane.
· Two Beckman Multimek 96s for high throughput automated filling of microtiter plates with 96-channel pipettor.
· Gene Machines Hi-Gro incubators for culture of bacterial cells in 96-well plates; includes aeration, heating and shaking.
· MWG Roboprep 2500 for automated preparation of plasmid DNA by alkaline lysis with 8-channel liquid-handling.
· Packard Multiprobe II for automated setup and cleanup of PCR reactions with 8-channel liquid-handling. Quantify plasmid DNA by UV absorbance or Pico Green fluorescence with the integrated Fusion microtiter plate reading fluorometer. Rearray cultures or samples in microtiter plates with use of the eight independent liquid-handling probes.
· ABI 3730xl, a 96-capillary instrument for fractionation of extension products from DNA sequencing PCR reactions. Output capacity is ca. 4400 templates per week.
· Retrieval of sequencing results by ftp from our server.
Genotyping
· ABI 3100 a 16-capillary instrument for fragment analysis, including microsatellites and single strands run under non-denaturing conditions (SSCPs). Data is uploaded by ftp to our Genemapper 3.7 workstation. Clients are trained in use of Genemapper for analyzing data.
Image Analysis
· Amersham Typhoon 9410, a combined phosphorimager/fluorescence imager with red, green and blue lasers for scanning gels and blots. This instrument has selectable resolution to 10 microns. ImageQuant data analysis software is available in CIF.
Gene Expression
· Affymetrix GeneChip® services for cDNA synthesis and cRNA labeling, processing equipment for hybridization, staining and scanning and software for first level data analysis.
· Affymetrix workstation for analyzing data from GeneChips®: includes GCOS and Data Mining Tool.
· Spotted microarray maker, a Bio-Rad VersArray ChipWriter Pro with quill-type pens from Telechem.
· Fluorescence scanner with red, green and blue lasers for reading spotted arrays after hybridization: Perkin Elmer ScanArray Express
· Workstation with Imagene 5.5 from Biodiscovery for analyzing spotted arrays.
· Spotted microarray maker and scanner from Genetic Microsystems (GMS 417, 418)
· ABI 7700 for quantitative PCR with real-time fluorescent monitoring of accumulating amplicon.
Flow Cytometry and Cell Sorting
· BD FACSAria for counting and/or sorting of cells from culture or dissociated tissue with fluorescence monitoring of cell surface, cytoplasmic or nuclear markers.
Protein Chemistry
· ABI Procise 492 for N-terminal protein sequencing by Edman degradation. Discontinued.
· ABI 433A for automated solid phase peptide synthesis. Discontinued.
· Amersham IPGPhor and 3 second dimension apparatuses for 2-D electrophoresis equipment. Please see Songqin Pan, CEPCEB academic coordinator in mass spectrometry.