Facility Services Table

The CCF is a cost-effective resource for the preparation of complex media as well as of the more common media.

By testing and purchasing an optimal fetal bovine serum batch, investigators have access to a consistent, quality-assured supply of at the most cost‑effective price.

Established cell lines are routinely obtained from a variety of sources and passaged in culture.

A wide array of established techniques is used to prepare primary cultures and to derive serially subcultured cell lines from them.

Immortalized B cells can be generated from human peripheral blood samples by transformation with Epstein Barr Virus (EBV).

Mycoplasma infestations of mammalian cell cultures can be detected by transferring their medium to indicator cultures of Vero monkey kidney cells and detecting mycoplasma DNA by fluorescence microscopy.

The Facility provides technical support, cells, reagents, and supplies for culturing mouse embryonic stem (ES) cells, and performs transfections and cloning to establish germline transmissible modified mouse ES cells to create knockout or knock-in mice

The Facility can produce hybridoma fusions, clone antibody-producing hybridomas, generate high titer monoclonal antibody (mAb)-containing culture supernatants, and bank hybridomas.

Viable cell samples are stored under liquid nitrogen (‑196°C) in cell banks with a total capacity of about 57,000 samples.

The Facility supports FCCC researchers in validating the integrity of their cell lines by providing a wide array of common stock cell lines that were obtained directly from approved sources

Cell surface staining using fluorescent-conjugated monoclonal antibodies can be analyzed.  Internal determinants can be analyzed if cells are first permeabilized prior to staining.

Cells with desired characteristics (distinctive protein expression, GFP+, etc.) can be isolated.

Measurement of Indo-1 loaded cells enables determination of intracellular calcium ion concentration and alteration after cell stimulation.

Samples (biochemical, cell culture or animal) are irradiated with specific doses.  Irradiations can be done to investigate radiobiologic mechanisms, to suppress immune response in animals or to sterilize cells or equipment.

Facility staff are available for consultation on the planning of experiments, including the dosimetry for custom set-ups.

Training is provided in accordance with PA-DEP regulations for staff to become independent users of the irradiators.

Preparation of histological sections from tissues provided by investigators

Preparation  of histological cryosections from animal tissues provided by investigators

H & E, and other classical histological techniques for microscopic evaluation of tissues and cells

Detection of  cancer-related proteins in tissue sections

Pathologists of the Facility will read slides and report on the abnormalities found when requested.

Web based database with all the cases signed-out by the Facility Director.  Found here.

Pathologists of the Facility will document microscopic findings when requested

Advanced computer-assisted image analyzers permit morphometric and densitometric analysis of tissue components and IHC reactions.

• Characterization of recombinant DNA expressed proteins and partially purified proteins at high sensitivity.
• Protein identification from affinity pull-down experiments.
• Characterization of post-translational modifications.
• Identify protein internal cleavage sites.

• Quantitative and qualitative analysis of metabolites and small molecules.
• Compound identification.
• Quantitation of drug from plasma samples.

• 2D gel comparative proteomics, high throughput protein identification by MALDI-TOF and using LC/MS/MS to identify complex samples.
• LC/MS/MS comparative proteomics with or without isotope labeling.
• GeLC/MS/MS comparative proteomics

• Fractionation of conditioned media, by size and by charge.
• Protein mixture purification.

• Hydrogen-deuterium exchange.
• Protein kinase substrate tagging methods.
• Quantitative analysis of new compounds using LC/MS/MS.

High resolution anatomic imaging of tumors and other anatomical structures in mice.

In vivo measurement of the signals from bioluminescent or fluorescence probes in mice.

In-vivo quantitative reconstruction in  three dimensions of the distribution of biologically targeted infrared fluorphores.

Provides for the detection and serial imaging of polyps in a mouse model for colon cancer.

Measure the regions of activation in the human brain when performing specific tasks. Used for behavioral studies.

The facility assists investigators in the development of robust assays for both basic science applications and prior to initiating screening.

The facility supports siRNA and small molecule screening by providing reagents, assay development support, training on instrumentation, and support during screen execution.

-RNAi library:
Thermo Fisher Dharmacon whole genome siRNA library comprising siRNA SMARTpools targeting approximately 22,000 genes.

-Small molecule libraries:
ChemDiv Diverse Collection – 50,000 compounds

-ICCB known Bioactives -480 compounds (Enzo Life Sciences; http://www.enzolifesciences.com/BML-2840/iccb-known-bioactives-library/)

The facility develops and executes clinical correlates at the request of investigators.  Please contact Margret Einarson  x. 215-728-2542 for additional information.

Provides simple way of imaging of protein molecules, macromolecular complexes, viral particles and isolated organels.

DNA or RNA molecules are spread on the suface of aqueous buffer either free or in a monolayer of denatured protein. Upon attachment to carbon-coated film, the molecules are contrasted by rotary shadowing with heavy metal.

Standard way of looking at the ultrastructure of cultured cells or tissues. Also can be used in conjunction with pre-embedding immunolabeling.

SEM is used to study the surface of the samples of interest. The object has to be first chemically fixed, dehydrated by critical point drying and further made electrically conductive by sputtering with platinum.

Samples of cell pelets or tissues are lightly chemically fixed and cryoprotected with sucrose. Upon freezing in liquid nitrogen, thin sections are cut at low temperature (-120°C) and labeled by indirect immunocytochemistry using gold particles as the electrondense marker (Tokuyasu method).

The Facility mostly provides experiment planning, all or most of the sample preparation and imaging. Help is also available with image processing and preparation for presentation.

The Facility requires that all users that wish to work on the Facility's instruments are trained by the Staff.

The users are encouraged to discuss their imaging needs with the Staff so that optimal sample preparation protocol, imaging mode and image processing can be selected and tuned for the particular application.

The recently acquired ASI  spectral head for Nikon Eclipse 800 microscope enables to map chromosomes in spreads by "chromosome painting" technology based on hybridization with fuorescent probes and subsequent spectral imaging and image processing.

Cryosamples of tissues and cell pellets are prepared using Tokuyasu method and semi-thin sections cut on a Leica cryotome.

The facility is equipped with an Eppendorf microinjector that is used for delivery of plasmids to cultured cells.

User supplied DNA templates (plasmids, PCR product) are analyzed to determine DNA sequence, typically generating over 700 bases of data.

Cell line species verification; computation of modal chromosome number; karyotypic analysis of blood, bone marrow, solid tumors, and cell lines; mapping the location of viral or transgene integrations, identification of chromosomal breakpoints, and detection of amplified or deleted genes in human, rat, and mouse metaphases by fluorescence in situ hybridization (FISH); interphase FISH; and chromosome painting and multiplex-FISH (M-FISH) to facilitate the interpretation of chromosome rearrangements.

Utilization of Affymetrix platform for various DNA copy number and loss of heterozygosity (LOH) analyses, pharmacogenetics, and promoter methylation studies.  SNP analysis for GWAS, using the Affymetrix platform, and array-CGH analysis of murine or human samples, using Agilent's DNA microarray-based technology.

The DNA Microarray Core provides full microarray hybridization services, including RNA isolation, probe labeling, hybridization, scanning and data extraction.  The raw data is then uploaded into the caArray database system for storage and management.  Users receive quantified microarray data sheets ready for further analysis.  This Core coordinates with the Biostatistics and Informatics Facility for microarray data mining and management.

MicroRNAs (miRNAs) have recently emerged as crucial regulator of gene expression, development, proliferation and differentiation, and the this Core provides microarray technology to miRNA expression analysis, thereby permitting sensitive and accurate global miRNA profiling.

This Core of the Genomics Facility performs cost-effective mouse genotyping services and qRT-PCR.  For genotyping, the Core performs DNA extraction from mouse tails and toe clips and develops, optimizes and performs allele-specific PCR assays for the genotyping of knockout, knock-in, and transgenic mouse strains. This service is carried out in collaboration with the Laboratory Animal Facility (LAF) with communication through the on-line mouse genotyping database that tracks the matings, genotyping results and animal inventory for each strain of mice.  The Core also offers HLA genotyping service for human samples.

Quantitative RT-PCR is offered for various purposes, including validation of DNA array gene expression data, quantification of gene expression, quantification of virus load, zygosity determination, quantitative analysis of alternative spliced transcripts, quantification of gene-specific DNA in immunoprecipitated ChIP assays, and validation of the effectiveness of siRNA transcription silencing.  The Core is equipped with several complementary technology platforms that allow for comprehensive and cost-effective analysis of variations and alterations such as SNPs, mutations, gene deletions, variable nucleotide tandem repeats, LOH, and CpG methylation.  These platforms include pyrosequencing (PSQ96MA, Biotage), capillary electrophoresis (CEQ8800, Beckman Coulter) and two real-time fluorescent PCR machines (ABI PRISM 7900 SDS, Applied Biosystems) in a 96-well, 384-well or low-density array format.

Instrumentation and expertise needed for the isolation of pure populations of cells from heterogeneous tissue specimens.  LCM services include identification and isolation of tumor cells or other cells of interest, as well as DNA, RNA and protein purification from LCM samples.  This Core is equipped with two LCM systems (PixCell II® and Veritas™, Molecular Devices), which are available for a wide range of applications, including LCM of specific immunostained or fluorescent cells. A SYBR Green assay is utilized to screen formalin-fixed paraffin-embedded (FFPE) tissue blocks for intact RNA that is suitable for microarray or RT-PCR analysis.  Amplification of limited quantities of total RNA from microdissected frozen and FFPE tissues is also available.