Sidney Kimmel Cancer Center

Shared Resources

Sidney Kimmel Cancer Center's investigators conduct their research in collaborative, interdisciplinary research programs and centers. Their efforts are supported by SKCC's Shared Resources.  

Bioimaging

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Mission

The goal of the Sidney Kimmel Cancer Center Bioimaging Shared Resource is to advance the scientific research programs of the Cancer Center by providing powerful, reliable, and readily accessible light microscopic image acquisition and analysis capabilities to SKCC investigators. The Bioimaging Shared Resource provides laser point-scanning and spinning disk confocal, TIRF (total internal refection fluorescence), and widefield epifluorescence microscopy capabilities allowing for multi-wavelength visualization and analysis of fixed and living specimens, Z series, single molecule events at surfaces and interfaces, as well as image analysis and processing expertise.

Overview

The Bioimaging Facility has:

  • Two point-scanning laser confocal microscopes (Nikon A1R+ and Nikon C2+) ideal for viewing fixed specimens with thicknesses up to several hundred microns, or observation of live samples. Most investigators use these systems, particularly for initial examination.
  • A spinning disk confocal/TIRF microscope (Andor/Nikon) specialized for short-term high-speed observation of live cells, particularly of the cell-substrate interface region.
  • A widefield epifluorescence microscope (Zeiss) for longer-term observation (minutes to hours) of multiple regions of interest in living samples.

Training, Protocol Development & Image Analysis

Our goal is to have all instruments fully operational and ready for usage to accommodate investigators' needs at all times. To this end, the SKCC Bioimaging staff will provide expertise and operate instruments for occasional users who may not need or want to acquire proficiency themselves. For more intensive prospective users, the Resource provides training on the use of all the systems and monitors their usage. Once trained and having satisfactorily demonstrated proficiency to Resource staff, the equipment is available on a 24/7 basis. To insure that skills are maintained, investigators who have not used the Resource equipment for several months are encouraged to schedule a brief refresher session - this may be required at Resource management discretion.

Advice on protocol development, filter and fluorophore choice is also available. Staff will assist with troubleshooting image quality and data quantification, providing information on applications custom-tailored to the individual investigator's needs.

Equipment Available

The confocal microscopes provide investigators with the ability to localize and determine extents of colocalization of multiple fluorescent signals in samples with thicknesses up to several hundred microns. In addition, more sophisticated procedures such as use of photoactivatable probes employing near-UV excitation, FRAP, FRET can be performed. The spectral detector in the A1R system allows for emission fingerprinting and separation of spectrally-similar fluorophores.

 

Nikon A1R with High Speed Resonant Scanner Confocal Microscope

  • Nikon TiE inverted microscope with PFS for image stability control
  • 10x, 20x, 40x oil, 60x oil and 100x oil objectives
  • 4 lasers with excitation lines at 405, 458, 488, 514, 561, and 640 nm
  • 2 GaAsP detectors and 2 high sensitivity PMTs
  • Spectral detector for resolution of very closely emitting fluorophores
  • DIC transmitted light
  • NIS Elements acquisition and analysis software with deconvolution module
  • Programmable X,Y,Z stage for multiple positions and stitching of large areas
  • z-stack, FRET, FRAP, photoactivation, time lapse functions, tiling
  • Tokai-Hit temperature and CO2-controlled chamber for live imaging
  • Anti-vibration isolation table

 

Nikon C2 Plus laser confocal microscope

  • Nikon TiE inverted microscope
  • 20x, 40x oil, and 60x oil objectives
  • 4 lasers with excitation lines at 405, 488, 561, and 640 nm
  • DIC transmitted light
  • NIS Elements acquisition and analysis software
  •  Programmable X,Y,Z stage for multiple positions and stitching of large areas
  • Z-stack, FRET, FRAP and time lapse functions, tiling
  • Anti-vibration isolation table

The TIRF (total internal refection fluorescence) microscopy system will permit high sensitivity, high speed imaging of biological phenomena occurring at the ventral surface (≤0.2 µm) of adherent cells without excitation further into the cell interior. Two discrete signals can be monitored simultaneously and a third can be imaged sequentially. The spinning disk confocal head is capable of continuous high-speed high-resolution imaging of live cells. Finally, photobleaching and photoactivation at all wavelengths can be employed in combination with all imaging modalities.

Andor/Nikon TIRF/Spinning Disk Confocal/Widefield Microscope

  • Nikon TiE inverted microscope with PFS for image stability control
  • 100x/1.49 NA TIRF objective
  • Andor laser control with 405, 488, 561 and 640 nm laser lines (all 100 mW and fast switching)
  • DIC transmitted light
  • Nikon TIRF E Motorized Illuminator
  • Yokogawa CSU-X1 spinning disk head for confocal imaging
  • Sutter Lambda DG4-Plus illuminator
  • Two Andor Ion X3 EM-CCD cameras each equipped with Dual-view2 splitters for simultaneous red/green imaging
  • Andor FRAPPA unit for photobleaching and photoactivation (operable under either Andor IQ or MetaMorph software)
  • Ludl programmable X,Y,Z stage with fast piezo Z drive for multiple positions and stitching of large areas
  • Z-stack, FRET, FRAP, photoactivation, time lapse functions, tiling
  • MetaMorph Premier image acquisition and analysis software
  • Okolab stage-top incubator for 35 mm dishes, 6-well plates, and 1" x 3" chamber slides
  • Anti-vibration air table

The widefield epifluorescence imaging system is specifically designed for high quality acquisition of live cell images over extended time periods (minutes to hours) with minimal photodamage under a controlled environment. Multiple regions of interest in a single sample can be repeatedly examined. The high speed Lambda DG4 filter changer allows for rapid excitation light changes to provide multiple signal acquisition with high temporal resolution. In addition, brightfield and DIC transmitted light images can be acquired.

Zeiss Axiovert 200M inverted microscope

  • 10x, 20x, 40x oil, 63x oil and 100x oil objectives
  • Sutter Lambda DG4 illuminator
  • DIC transmitted light
  • Andor Zyla sCMOS camera
  • MetaMorph Premier image acquisition and analysis software
  • Prior Proscan III programmable X,Y,Z stage for multiple positions and stitching of large areas
  • Time lapse functions, tiling
  • Okolab environmental chamber
  • Programmable pump and perfusion chamber
  • Anti-vibration isolation table

Capability can be implemented: investigators with a need for microinjection of molecules into individual cells or organisms should contact Resource personnel for further information and consultation.

Fees

All microscope systems have the same hourly rate (see table below) and technical assistance with operation of the microscopes is available ($25/hr on all systems). The minimum signup time for the microscopes or assistance is one hour:

SKCC TJU non-SKCC Non-TJU Academic Non-TJU Commercial
$25/hr $35/hr $50/hr $100/hr

In view of heavy demand for Facility time and to insure that equipment is available when investigators' samples are ready:

  • Please keep to the appointment start and end times you have reserved.
  • If you are more than 15 minutes late and you do not call, your appointment time will be given to the next person wishing to use the instrument on a first-come-first-served basis. You are responsible for calling if you are going to be late.
  • If you do not show up for your reserved time or you do not call to cancel 24 hours in advance, your laboratory will be charged for the first hour and your reservation will be given to the next person wishing to use the facility on a first-come-first-served basis.
  • If you need to use the facility on a short notice, please check with the facility staff and/or use the waiting list reservation link in the calendar.
  • On behalf of your colleagues and all Facility users, thank you for your cooperation.

Please feel free to contact us if you have any questions or suggestions.

PUBLICATION ACKNOWLEDGEMENT. (Very Important)  To accurately reflect the assistance the Resource plays in your research and to help assure its continued funding, please be sure to include the following Resource name and grant number in the acknowledgment section of all publications:

Bioimaging Shared Resource of the Sidney Kimmel Cancer Center (NCI 5 P30 CA-56036), and any staff (as appropriate).

Guidelines

New Users:

  • All new users must register with the facility to discuss usage of their samples
  • All users must be trained by the facility staff. After individuals have been trained and demonstrated proficiency they can access the facility 24/7.

Reservations:

  • Facility equipment is reserved through the Bioimaging Shared Resources reservation calendar online system on a first come, first served policy.
  • Cancellations can be made online up to 24 hrs prior to the reservation time. After that time you must contact the facility or you will be charged for the first hour of your appointment.
  • A waiting list has been implemented for those wishing to use the facility on a short notice.
  • Confocal microscopes cannot be reserved for more than three continuous hours during regular facility hours to allow broad access. If there is a special need, please contact staff.

Facility access:

  • The facility is open Monday thru Friday from 9AM to 5PM.
  • An individual access code number will be assigned to independent users needing access to the Facility after hours.

Use of the equipment:

  • No one can use the equipment without authorization from the facility staff.
  • If you were the last person scheduled for the day, always check the reservation calendar for late signups before turning off all equipment.
  • If you have to cancel your appointment on short notice after regular hours you must come to the facility as soon as possible and inform the person using the system to shut it down upon completion. The equipment must not be left on overnight!
  • Please notify facility staff of any unusual event, spill, and/or noise as soon as possible.
  • Please be aware of other users coming after you and finish on-time. This includes data transfer time.

Data Storage:

  • There is no long term storage of data at the facility. All users are responsible for the proper backup of their data.
  • Short term data storage is allowed as long as there is space on the hard drives but please remove your files within 2 weeks, at the latest. Periodic data purges are often required to ensure enough space is available for all users.

Contact

James Keen, PhD
Director
(215) 503-8982
912 BLSB
233 South 10th Street
Philadelphia, PA 19107
Maria Covarrubias, PhD
(215) 503-4770
Bioimaging@mail.jci.tju.edu
Bioimaging Reservation System

Biostatistics

Achievements

The Biostatistics Shared Resource continues to play a major role in collaborative efforts and project leadership across the cancer center and the university.  The Core has participated in the development of grant applications, in the analysis of data and publication of manuscripts, and in the development of IIT protocols developed with Medical Oncology, Radiation Oncology, and other clinical faculty.  Core faculty continue to serve as members of the cancer center clinical research review committee. 

The Core is currently or was funded over the past year as PI/ co-Investigators on grants with SKCC investigators as listed in the table to the right. Items in BOLD are multi-investigator/P01/Consortium projects.

Funding from the SKCC core grant supported data analysis work on 20 intramurally funded research projects of SKCC investigators.

The core continues to support grant submissions for the SKCC, with active roles in preparation of 28 applications for submission to NCI, DOD, AHRQ, PCORI, and other agencies.   In addition, core faculty assisted in the design of 23 research protocols.  Funding for grant and protocol development was provided from institutional support.

Changes in Leadership & Capabilities. The core facility currently consists of 5 faculty and 2 staff.  This is a reduction in staff from 5 in the previous year due to the completion of some externally funded projects.  The availability of staff to support SKCC activities remains the same.  

Research Grants of SKCC Investigators
Supporting Biostatistics Faculty & Staff

  Funding Source
Ronald Myers
PCORI
Andrew Alpin NIH/NCI
Andrew Alpin NIH/NCI
Jonathan Brody NIH/NCI
Scott Waldman Commonwealth of PA
(nonformula funds)
Hallgeir Rui Komen Foundation
Hallgeir Rui Komen Foundation
(subcontract from Duke University)
Richard Pestell (Core Grant)
NIH/NCI
Marja Nevalainen NIH/NCI
Marja Nevalainen Novartis
Vittorio Maio Emilia Romagna Regional Government

Cancer Genomics

Mission

To provide researchers the most comprehensive data efficiently through the utilization of cutting edge technology.

Our goal is to provide researchers a full service laboratory including sample preparation through the completion of data analysis.

We offer a full array of services:

  • Next-Generation sequencing applications
  • Traditional DNA sequence analysis
  • mRNA, microRNA, genome-wide SNP assays including Cytoscan, OncoScan
  • Analytical microchips for disease gene pathways discovery and circulating tumor cells
  • Comprehensive data analyses including interpretation allowing the delineation of differences between normal and diseased states
  • Quality Analysis
  • Sample Isolation
  • Real-Time PCR
SKCC Genomic Laboratory

Our Laboratory

The SKCC Genomic Laboratory at the Kimmel Cancer Center was initiated in July 2006 to provide a full array of services, from traditional DNA sequence analysis to the most recent mRNA, microRNA and genome-wide SNP assay capabilities allowing the delineation of differences between normal and diseased states. The facility is dedicated to meeting the current and future needs of both researchers and clinicians and regularly implements new technologies and methods to provide the highest level of service.  An integral role of the facility also is to test new equipment and assays in collaboration with biotech companies.

The facility comprises two central components:

  • the Genomics Laboratory, which provides instrumentation and expertise for nucleic acid extraction, quality assessment of total RNA and genomic DNA, RNA global transcription patterns, miRNA profiling, genome-wide SNP genotyping, mutation detection and DNA sequence analysis.
  • the Computational Laboratory, which undertakes all bioinformatics data analysis, software development, and data management.

Both of these components are run by research teams who provide training and support for collaborators/users at the SKCC, TJU and elsewhere.

Featured Technologies

The Illumina NextSeq 500 sequencer is a high throughput sequencing instrument capable of producing between ~19 - 120 gigabases of sequence with the option of running in either Rapid Run or Mid Output mode. Sequence from a variety of sample types derived from virtually any DNA or RNA sample. The read size per fragment is up to 150 bases, and the paired-end module allows for sequencing of up to 150 bases at each fragment end. The applications for which Illumina sequencing is useful include, but are not limited to: Whole genome sequencing, SNP Genotyping and CNV analysis, mRNA-seq, small RNA-seq and epigenetic analysis (methyl-seq, ChIPseq).

The Illumina platforms support the sequencing of samples from a variety of starting materials including genomic DNA (single-read, paired-end reads, and mate-pair sequencing) PCR products, mRNA, and small RNA. The Core offers full library preparation services for most Illumina libraries. Please contact us for additional information and download the Illumina Library Prep Request form for sample submission.

An Illumina NGS User Agreement form should also be filled out completely and dropped off to room 1009 of the BLSB with your samples. When filling out the Agreement form make sure to include all pertinent information, including sample names, pooling/indexing information, and any custom sequencing primers required for the run. We ask that you provide any QC performed on the completed library. The Genomics Core does offer a library quantification package to check library quality and will QC all samples that are submitted to determine if they can continue onto sequencing.

Illumina Sequencing Applications

Single Read Sequencing - Single-read sequencing is the simplest way to utilize Illumina’s systems whether you need to sequence an entire genome or a large candidate region.

Paired-end Sequencing - Paired-end sequencing generates a second read from the opposite end of each fragment. The benefit to researchers, besides more data, is positional information, alternate splice junctions, insertion/deletions, etc. Paired-end sequencing is typically performed on fragments between 200-500 bases in size; however, Illumina’s Mate-pair protocol utilizes an insert size of 2-5kb to facilitate identification of large structural variants and repeats, and assist in de novo assembly.

Transcriptome -This analysis includes PolyA-selected mRNA-seq, tag profiling, directional sequencing, small RNA discovery and whole transcriptome analysis. Samples are composed of enriched mRNA via ribosomal RNA (rRNA)-depleted sample prep. Interrogate splice variants, coding SNPs, and relative expression levels of transcripts are common output.

Targeted Capture - Solution based methods allow researchers to isolate regions of interest from genomic DNA for high-throughput sequencing. Off-the-shelf whole human exome kits are available, as well as custom designs, ranging in size from 200Kb to 62Mb. The Core has experience with Agilent SureSelect Human All Exon and Illumina products. We also offers whole human exome, and custom capture kits as well.

Epigenetic Analysis - Researchers have developed protocols that allow for the examination of CpG methylation, histone modifications, chromatin structure, or DNA-protein interactions using Illumina’s sequencing technology. ChIP-Seq uses a combination of chromatin immunoprecipitation and Illumina sequencing to quantify in vivo protein-DNA interactions on a genome-wide scale and Methyl-Seq allows researchers to map genome-wide methylation patterns. RIP-seq and CLIP-seq are also offered.

MiSeq Applications

The MiSeq™ system integrates multiple aspects of the traditional sequencing workflow including clonal amplification, sequencing, data analysis and variant calling all into one simple interface, delivering biologically meaningful results faster than ever and with unsurpassed cost-per-base efficiency. Common MiSeq™ services support applications including but not limited to:

•     Highly Multiplexed PCR Amplicon Sequencing

•     Cancer and Custom Gene Panel Assays

•     Targeted Re-sequencing (including Agilent’s Haloplex technology)

•     De Novo Bacterial Sequencing

•     Small RNA Sequencing

•     16S Metagenomics

Check out the Illumina website for more information.

Services

DNA isolation and purification from human and animal matrices are performed daily using Chemagen’s automation extraction robot and their proprietary magnetic bead technology.

Using the chemagic magnetic separation module, DNA is extracted from many different biological matrices including but not limited to

  • whole blood
  • buffy coat
  • buccal swabs
  • saliva
  • bacteria
  • human and animal tissue including mouse tails
  • formalin fixed paraffin embedded tissue
  • cell culture fluid and cells
  • plasmids
  • PCR-products
  • amniotic fluid
  • plants
  • mRNA extraction is also offered

The Agilent Bioanalyzer is used for rapid analysis of RNA and DNA samples. The system permits accurate sizing and quantitation of samples within minutes of loading and consumes only small amounts of material. This unit is especially important in assessing RNA quality and amounts prior to cDNA synthesis and labeling for microarray applications. In addition to characterizing total RNA used as starting material, the Bioanalyzer is able to check the quality of the RNA probe generated, check the status during labeling and fragmentation, and measure the amount which should be used in hybridization.

 

The Ion AmpliSeq Cancer Panel includes 50 genes, which are linked to targeted anti-cancer drugs currently on the market. Tumor DNA is extracted from a formalin-fixed paraffin embedded (FFPE) tissue sample. Next generation sequencing (NGS) is performed to find variants and small insertions/deletions, including those present in small amounts of tissue and not detectable using traditional Sanger DNA sequencing. The results coupled with bioinformatics provide a detailed molecular profile of the tumor that includes a list of all mutations. The report, delivered within 14 working days, details the mutational signature and provides the treating oncologist with an evidence-based list of therapies currently on the market, which facilitates a targeted approach to treatment for a specific tumor genotype.

 

Whole Exome Sequencing (WES) Many cancer-causing variants and mutations are found within exonic, or protein coding regions, which are critical in the development of human cancers. WES enables a closer look at these regions by analyzing of all coding regions (exons) of the genome simultaneously using NGS-based techniques. Approximately 180,000 exons in the human genome (22,000 genes) are analyzed, including mitochondrial genome screening.  The test requires 200 mg of fresh frozen tumor tissue or 10 cc of peripheral blood. The report details the precise mutational signature of the cancer and is delivered within 6 weeks.

HTA 2.0 provides the coverage of up to 285,000 full-length transcripts, which include 245,000 coding transcripts, 40,000 non-coding transcripts and 339,000 probe sets covering exon-exon junctions. Up to 6.0 million distinct probes on the array maximize exon coverage in order to measure all transcript isoforms (70% and 30% of the probes cover coding transcripts and exon-exon splice junctions and non-coding transcripts, respectively). This high-resolution array design requires 50 to 500 ng of total RNA input and is optimized for both FFPE and fresh frozen samples.

 

OncoScan FFPE Assay kit, based on Molecular Inversion Probe (MIP), exposes genome-wide copy number and loss-of-heterozygosity (LOH), and the status of frequently tested somatic mutations with its enhanced resolution of ~900 cancer genes. The test recently released by Affymetrix identifies copy number changes associated with tumor characteristics and examines the association of amplification events with stage and grade of disease.

The ability to quantitate PCR products as a measurement of the amount of template which was present at the beginning of the reaction has been hampered by the need to make measurements in the linear phase of the reaction, between cycle numbers, which will differ even among identical reactions in different tubes. Real-time quantitative PCR, using fluorescent probes and a detector such as the Applied Biosystems 7900HT, permits relative and absolute quantitation of transcripts with increased sensitivity, automatic data collection and multi-color capability. Subtle changes in transcript amount can be detected, and 96 or 384 samples can be run simultaneously, greatly facilitating gene expression studies.

The sequencing workhorse of the Facility is an Applied Biosystems 3730 Genetic Analyzer, a 48-capillary electrophoresis unit, which can perform hundreds of sequencing reactions per day. Runs in excess of 700 bases can be obtained in 1.0 hour and even longer runs can be obtained by varying run conditions. Plasmids, large insert clones and PCR products of a variety of sizes can be analyzed using BigDye Terminator Kit and cycle sequencing protocols. DNA sequencing-based services provided by the Facility include:

  • Direct PCR product sequencing using either PCR primers or an internal primer
  • PCR product purification and sequencing
  • Direct sequencing of plasmid, cosmid, P1, BAC, PAC and other clones.
  • Plasmid/BAC/cosmid, etc. template DNA isolation and sequencing.
  • Entire clone insert sequencing using primer walking strategy.

The Facility provides microsatellite analysis using the ABI 3730 platform. The microsatellite assay detects microsatellite marker repeat lengths in genomic DNA using fluorescently labeled PCR reactions on the ABI 3730 sequencer. Mouse genotyping via marker-assisted profiling of selected informative microsatellite markers is available.

Numerous options for characterizing SNPs are available including TaqMan-based genotyping and the Affymetrix GeneChip platform for high-throughput genotyping. Custom SNP panels can be designed for a particular project. Choosing the right platform starts with the list of SNPs to be tested and Facility team can aid in exploring custom multiplex options.

The Facility provides the TaqMan-based assay with readouts of the genotypes using the AB 7900HT instrument. Thousands of verified SNPs are available as reagents in which the PCR primers, conditions and allele-specific probes all have been verified (Assays-on-Demand™). Those SNPs not already included as “off-the-shelf” products can be ordered from the database and developed as verified reagents as well (Assays-by-Design™).

 

In instances in which a genome-wide genotype is preferred, the facility utilizes the Affymetrix 250K and SNP 6.0 GeneChips which provide the capability to assay large numbers of alleles in parallel. The array platform provides comprehensive genome coverage at high-resolution necessary for genome-wide association studies, loss of heterozygosity and gene copy number variation. The assay requires 500 ng genomic DNA as starting material.

The facility offers standard analysis services for gene expression microarray data including differential expression analysis and cluster analysis. Advanced bioinformatics services are also available to provide contextual data analysis using tools such as GeneSpring, Gene Set Enrichment Analysis and Ingenuity Pathways. The application of these computational tools is tailored to provide comprehensive analysis to support studies using gene expression, genotype and genomic copy number data.

PRICING. Please note that the prices listed below are estimations and are subject to change. We recommend contacting our laboratory for consultations regarding Next Generation Sequencing and Affymetrix Microarray projects. Volume discounts are applied to all of our services, and they are not reflected in the estimations provided below. All pricing indicates per sample unless otherwise noted.

Data Analysis is $125/hour

NEXT GENERATION SEQUENCING

NextSeq 500 – Rapid Run mode

# of Cycles

Full flowcell
(2 lanes)

Split flowcell
(1 lane)

Single Read

50 bp
10

$

$

 

100 bp

$

$

Paired-end Read

50 bp

$

$

 

100 bp

$

$

 

 

 

 

NextSeq 500 – High Output mode

50 cycle run

100 cycle run

 

Single Read

$

$

*full flowcell =
8 lanes

Paired-end Read

$

$

 

 

 

 

 

 

1x36 /
2x25 bases

1x300 /
2x150 bases

1x500 /
2x250 bases

MiSeq

$

$

$

MiSeq Nano v2 (1M reads)

$

$

$

MiSeq Micro v2 (4M reads)

$

$

-

LIBRARY PREPARATION

DNA Libraries

Quantity

Volume

QC

Price

TruSeq DNA

1 ug

< 50 ul

260/280: 1.8-2.0

$

TruSeq ChIP-seq DNA

5-10 ng

< 50 ul

260/280: 1.8-2.0

$

Nextera DNA
24 sample minimum

50 ng/1 ng

< 20 ul

260/280: 1.8-2.0

$

Nextera XT DNA
24 sample minimum

1 ng

< 5 ul

260/280: 1.8-2.0

$

 

 

 

 

 

RNA Libraries

 

 

 

 

TruSeq RNA

0.1-4.0 ug

< 50 ul

RIN: 8.0-10.0

$

ScriptSeq Complete Gold (human/mouse/rat)
also in low input
6 sample minimum

1-5 ug

< 10 ul

RIN: 8.0-10.0

$

Please note we are not limited to the Arrays listed below please call if you do not see what you are looking for.

Affymetrix Chip

Price

Human Gene Array 2.0

$550.00

Human Transcriptome Array 2.0

$680.00

Human Transcriptome Array 2.0 Pico Affy reagents

$605.00

Human Transcriptome Array 2.0 WT Affy reagents

$605.00

Mouse Gene Array 2.0 Affy

$400.00

Mouse Gene Array 2.0

$550.00

Rat Gene Array 2.0

$550.00

Drossophila Gene 1.0 ST

$600.00

Mouse Transcriptome Array

$650.00

miRNA 4.0 Array

$500.00

Oncoscan

$750.00

Traditional Sanger Sequencing

$6.25

Real-Time PCR / Plate

$60.00

Agilent Tape Station/ Lane

$6.00

Agilent per chip (12 samples)

$60.00

Quibit Analysis

$12.00

DNA Extraction

$45.00

RNA Extraction

$75.00

CONTACT

Paolo M. Fortina, MD, PhD
(215) 955-0683
(215) 503-9142 fax
Bluemle Life Sciences Building
Room 1009
Philadelphia, PA 19107
Melanie Kelly
(215) 955-9572
Bluemle Life Sciences Building
Room 1009
Philadelphia, PA 19107
Adam Ertel
(215) 503-7452
Bluemle Life Sciences Building
Room 1009
Philadelphia, PA 19107

Flow Cytometry

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The Sidney Kimmel Cancer Center facility provides state-of-the-art fluorescence activated cell sorting and analysis capabilities to investigators of the Sidney Kimmel Cancer Center and the Philadelphia region. The most commonly used applications are multi-color cell surface phenotyping, detection of intracellular cytokines and signaling molecules, transfection measurements, studies of apoptosis, cell cycle analysis, cell proliferation, and real time analysis of Ca2+ mobilization kinetics. The sorters, analyzers, and workstations allow for affordable, reliable, and accurate characterization of a wide variety of biological samples.

The services provided by the facility can be tailored to suit experimental designs in a variety of fields. We provide consultation on current protocols, analysis techniques, and data presentation. This resource plays a critical role in assisting SKCC members performing various research projects directly related to the understanding of the biology and treatment of cancer. Furthermore the facility supports projects from investigators in Biochemistry, Genetics, Immunology, Medicine, Microbiology, Molecular Biology, Neurology, Pathology, Pharmacology, Surgery, and many other scientific fields.

The equipment of the FCSR includes a BD FACSAria special order speed sorter equipped with 2 lasers, 8 colors and has the potential to upgrade to more parameters. The Beckman Coulter MoFlo high-speed cell sorter has been retired as it needs constant repair and maintaining the service contract is not cost effective. The BD LSRII Analyzer is a workhorse logging ~8 hours/day analysis.  All data is digitally processed in FACSDiva v.6.6 software and generates FCS3.0 files that can be analyzed post-acquisition in FlowJo or FACSDiva; and 4). BD FACSCalibur Benchtop Analyzer equipped with 2 lasers is being used mostly for 1-2 color analysis.

With the installation of a biosafety containment, the FACSAria sorter allows for sorting of oncogenic and infectious materials such as primary human cells, human cancer cells and cells over-expressing oncogenes and cell infected with viruses.  This greatly facilitates the studies by SKCC members and other users.

In addition to providing priority services to meet the research needs of the SKCC members, the FCSR offer high quality flow cytometric analysis services to other investigators throughout the Thomas Jefferson University Campus as well as its affiliated research centers and hospitals.  The KCC FCSR is the only core facility of its kind on the entire campus. The FCSR also provided flow cytometric services including data acquisition and sorting to investigators from neighboring institutions including University of Pennsylvania, Temple University, Drexel University, and the University of Delaware. Additionally, the FCSR provided service to Johnson and Johnson, Vitae Pharmaceuticals, DuPont Children’s Hospital, Nemours Foundation, and Cooper Hospital.  The FCSR is centrally located on the TJU campus, in a dedicated laboratory space in the Bluemle Life Sciences Building (BLSB), which allows trained Cancer Center members 24-hour access to the analytical cytometers, workstations, and cell counters. The FCSR is the only shared resource that provides access to all Thomas Jefferson University investigators.

CONTACT

Jianke Zhang, PhD
Director  
BLSB, Room 606
233 S. 10th Street
Philadelphia, PA 19107
Lei Yu, PhD
(215) 503-4556
 

Informatics

The Informatics Shared Resource (ISR) serves as a biomedical research informatics resource for Sidney Kimmel Cancer Center (SKCC)'s basic, clinical, and translational investigators. This support includes infrastructural provisioning, software development or acquisition, and consultative collaboration. ISR services are available directly to peer reviewed funded cancer investigators, or indirectly to other cancer center core facilities, thereby providing services to all program members. The ISR also provides informatics support for the clinical research activities of the Sidney Kimmel Cancer Center Network of community hospitals.

More specifically, the ISR supports cancer center research by developing and/or deploying:

  1. Clinical trials applications to give clinical researchers the tools to manage clinical trials data, including mandated reporting.
  2. Biospecimen repository applications to help tissue bank staff manage specimen accessioning and distribution, and provide investigators with an ordering mechanism and information characterizing specimens available for research.
  3. Research Data Analytics (data warehousing and mining applications) to provide cancer researchers with a research data mart that integrates clinical, biospecimen, cancer registry, clinical trials, and genomic data for cohort identification and hypothesis generation.
  4. Infrastructure and applications for other SKCC shared resources to facilitate access to their services. The ISR thus provides SKCC investigators with ready access to integrated comprehensive information on clinical trials, cancer patients, and research specimens, as well as providing a single portal for requesting equipment and services from SKCC shared resources.

In all its activities, the ISR recognizes interoperability as crucial to the sharing of research data and resources to promote efficient cancer research, and utilizes standards articulated by the NCI and the biomedical informatics community. Software applications are hosted on servers with networked storage located at a commercial data center contracted by the University, providing professional data center security and disaster recovery services. The ISR employs best practices with regard to data privacy and security, complying with the Common Rule, HIPAA, and state regulations.

CONTACT

Jack London, PhD
Resource Director
(215) 503-4599

BLSB, Room 812
233 S. 10th Street
Philadelphia, PA 19107


Laboratory Animal

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The Laboratory Animal Facility of the Sidney Kimmel Cancer Center provides housing and quality maintenance and care for laboratory animals used by the SKCC Staff. The facility also provides technical expertise in small animal surgery, administration of chemical carcinogens, and in-colony health surveillance.


CONTACT

Linda Siracusa, PhD
Resource Director
(215) 503-4536

BLSB, Room 1150
233 S. 10th Street
Philadelphia, PA 19107

Judith Daviau, DVM
Director, Animal Resources
(215) 503-5885
 

Small Animal Imaging

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The Small Animal Imaging core facility is a state of the art in vivo imaging lab dedicated for small animal research. Housing the Philips Mosaic Positron Emission Tomography (PET) system and the Imtek Inc. MicroCAT II Computed Tomography (CT) system; this lab provides accurate molecular and anatomical fused imaging. These imaging modalities offer unprecedented opportunities to study in vivo small animal models of disease; providing more accurate assessment of disease progression and response to therapy.

With support from the entire Department of Radiology, the lab will work with individual investigators to define experiments, imaging protocols, and quantification techniques to meet their individual needs. Please contact the facility for more information.

Equipment

Positron Emission Tomography (PET) imaging provides in vivo functional images of molecular processes; offering the potential to detect disease at the cellular level before anatomical changes occur. To generate an image, a tracer amount of a radio-labeled probe is injected into the subject. The bio-chemical pathways of the body distribute the isotope. The distribution of the probe is acquired and reconstructed into 3D volumetric images.

Philips MOSAIC PET
Specifications:
14,456 GSO 2x2x10mm3 crystals
288 photomultiplier tubes
128mm transverse FOV
120mm axial FOV
2.0 mm resolution (approximate)
Example PET Imaging Probes:
COMPOUND PURPOSE
F-18 FDG Glucose metabolism
Cu-64 VIP Oncogene expression
Cu-64 PNA Oncogene expression
Cu-64 ATSM Hypoxia
 

Computed Tomography (CT) imaging provides high resolution in vivo anatomical images. To generate an image, an external x-ray source is rotated around the subject. The attenuation projections are acquired and reconstructed into 3D volumetric images of tissue densities. Various contrast agents can be employed to provide enhanced discrimination of structures with similar densities.

The CT images can be analyzed alone or can be fused with PET images to provide more precise localization and quantification.

Imteck Inc. MicroCAT II CT
Specifications:
68x90mm2 CCD detector
50mm transverse FOV
90mm axial FOV
50um resolution (capable)

 

Imaging Examples

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These FDG PET images, in coronal view, show the progression of a flank tumor in the same mouse over a period of four weeks.

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This image is a 3D rendering of a bone segmented CT image fused with a PET FDG image showing a Glioma on the left shoulder. Courtesy of Philips.

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This fused PET-CT image, in transverse view, shows cardiac FDG uptake from the PET slice in color overlaid on a CT slice in gray.

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This fused PET-CT image, in transverse view, shows flank tumor uptake of Cu-64 labeled CyclinD specific PNA from the PET slice in color overlaid on a CT slice in gray.

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This FDG PET image, in sagital view, shows uptake in the colon of corresponding polyps which were verified in resection.

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These FDG PET images, in coronal view, show normal glucose metabolism in a healthy mouse.

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These FDG PET images, in coronal view, show an abnormal spleen and abdomen lymph node uptake in a mouse with advanced leukemia.

CONTACT

Mathew Thakur, PhD
Director
(215) 503-7874
474 JAH
1020 Locust Street
Philadelphia, PA 19107
Laboratory
(215) 503-1750
 

Translational Research/Pathology

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The Translational Research/Pathology Shared Resource Core Facility provides outstanding full range histopathology services complemented by access to unique banked tissue collections and Laser Capture Microdissection of tissues to capture individual cells for KCC members and external users. The Translational Research/Pathology Shared Resource Facility is used by over 100 investigators and has provided key data that support numerous publications and grant applications.

Mission

  • Tissue Processing and Histology Services; Frozen and Fixed Tissues
  • Immunohistochemical Staining of Tissue Sections
  • Tissue Procurement, Banking, and Distribution
  • Microdissection of Tissues and Laser Capture of Individual Cells
  • Quality Assurance and Clinical-Pathologic Data Collection

Services

The facility provides a full range of histopathological services including sample processing, slide preparation and staining of human and animal tissues or cell samples. Automated processing and tissue stainers provide highly reproducible results and allow co-registration of staining in the facility with analysis carried out in clinical pathology laboratories. Immunohistochemical staining is performed on paraffin sections, frozen tissue or cytologic preparations, utilizing a broad range of optimized commercial antibodies or antibodies provided by the investigator to be optimized.

Histology and Immunohistochemistry request forms with relevant materials should be delivered to room 815 in BLSB.

Frozen and paraffin embedded tissues are available to participating scientists either from the tissue bank, or from paraffin block archives. The banking was expanded to collect body fluids and blood for a subset of patients. Improved web-based clinical data systems for the tumor bank utilizes the NCI sponsored "Cancer Biomedical Grid" (CaBIG) and "CaTissue" database application that has been established at the Sidney Kimmel Cancer Center. The caBIG/caTISSUE system allows access to de-identified clinical information for each human tissue specimen in the Translational Research/Pathology Shared Resource. Where appropriate and IRB approved, clinical-pathologic data can be requested.

For database searching of Tissue Bank, please contact Dr. Chatterjee at (215) 503-4876 located in room 812/BLSB. Requests for archived blocks, please contact Cheryl Morris at (215) 955-5695 located in room 307F/Pavilion. For new tissue requests, please contact Dr. McCue at (215) 955-5588 or contact a collaborating pathologist so that the archive search can be scheduled.

Specimens requiring microdissection or laser capture of individual cell types are processed via microscopic evaluation by the Core's surgical pathologists. All specimens are reviewed by organ type, tumor content, and tissue viability. Microdissection requests and requests for Pathology review of sections and slides should be made to individual collaborating surgical pathologists. Laser Microdissection requests should be discussed with Dr. Mark Curtis at (215) 955-6206.

Instructions/Forms

Note: all protocols must have IRB approval before requesting service.

Instructions for tissue sample preparation and submission:

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CONTACT

233 S. Tenth Street
Bluemle Life Sciences Building, Room 815
Philadelphia, PA 19107
(215) 503-3858

Monday - Friday, 9:00 AM - 5:00 PM

Wei Jiang, MD
Director
(215) 503-5665
132 South 10th Street
Main Building, 285L
Philadelphia, PA 19107
Haifeng Yang. PhD
Co-Director
(215) 503-6163
1020 Locust Street
JAH 336D
Philadelphia, PA 19107
Charalambos C. Solomides, MD
Co-Director
(215) 503-6202
132 S. 10th Street
Main Building, Suite 260E
Philadelphia, PA 19107
Stephen C. Peiper, MD
Associate Director, Translational Research
Chair and Peter A. Herbut Professor
Department of Pathology, Anatomy and Cell Biology
(215) 955-5060
1020 Locust Street
Jefferson Alumni Hall, Suite 279
Philadelphia, PA 19107

X-ray Crystallography & Molecular Characterization

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This facility serves the needs of SKCC research programs in crystallization, X-ray data collection, structure determination, refinement and structural analysis of macromolecules. The facility has HydraIIPlusOne and Oryx8 crystallization robots for high-throughput crystallization screening and maintains two X-ray diffractometers: an Enhance Ultra sealed tube X-ray generator with Osmic Confocal Max-Flux optics, Xcalibur kappa 4-circle diffractometer, Cryojet XL and a 165 mm Onyx CCD detector and a new (installed in January 2015) Rigaku MicroMax-007HF microfocus rotating anode X-ray generator dual equipped for data collection from macromolecular crystals and Small Angle X-Ray Scattering (SAXS). The left port of this instrument, dedicated to X-ray data collection from macromolecular crystals, is equipped with high focusing mirrors and a new ultrafast PILATUS 200K Hybrid Pixel Array Detector and a X-stream 2000 cryogenic system, while the right port hosts a new BioSAXS-2000 2D Kratky SAXS system.

The facility also provides access to instrumentation for biophysical characterization of proteins, and protein/protein and protein/DNA interactions. These instruments include a Beckman Coulter Analytical Ultracentrifuge (ProteomeLab XL-I Protein Characterization System), a JASCO J-810 Spectropolarimeter, a BIACORE 3000 SPR biosensor, a KinExA 3000, and two Isothermal Titration Calorimeters: MicroCal-ITC and a TA Instruments Nano-ITC.

CONTACT

Gino Cingolani, PhD
Director, X-ray Crystallography
826 BLSB
(215) 503-4573

822 BLSB
233 S. 10th Street
Philadelphia, PA 19107
Michael Root, MD, PhD
Director, Molecular Characterization
802 BLSB
(215) 503-4564
X-ray Crystallography &
Molecular Characterization Resource
Reservation System
Anshul Bhardwaj, PhD
Facility Manager
(215) 503-4587