Office of the Vice President for Research has negotiated an exclusive agreement with Fox Chase Cancer Center Microarray Facility. This agreement will allow Temple researchers to utilize services provided by this facility at same cost as Fox Chase researchers.
Overview of the facility:
The Fox Chase Cancer Center DNA microarray core facility was established in 1999. The facility produces high quality human, mouse and yeast microarrays and provides researchers with technical expertise in array design, probe hybridization and data analysis. The equipments include a capillary-based DNA micorarrayer with automate plate loaders (OmniGrid systems) from GeneMachines and a confocal laser scanner (GMS 428). The OmniGrid microarrayer has capacity of holding 72 plates and prints 100 slides in one run. The GMS 428 scans and records microarray images at 10-l1m resolution. The facility has also a BioMek 2000 (Beckmen) liquid handling system and a 4-heads MJ PCR machine for cDNA clone replication and PCR amplification. The FCCC DNA Microarray Facility has been cited in several publications using the facility resource.
The facility has acquired a human cDNA library (~40,000 clones) from Research Genetics and a mouse cDNA library from NIH (NIA 15k mouse clones). All clones have been replicated and PCR amplified. Human and mouse microarrays containing 40,000, 15,000 cDNA clones, respectively, have been produced and used by FCCC investigators. Recently, the facility introduced a line of oligo array products including 30,000 human and 6,000 yeast 50mers oligo arrays from MWG Biotechnology, as well as 32,000 70mer mouse genome oligo set from Qiagen/Operon. The facility recently acquired a rat oligo sets to complete the oligo array product line in the near future. Fox Chase has developed and standardized all micro array process, including microarray printing, RNA probe labeling and hybridization.
In summary, the facility provides investigators, with high quality of both cDNA and oligo array line products such as human, mouse and yeast array slides, customer printing and labeling kit. Full array service including probe labeling, hybridization and image process is also available.
Bioinformatics Core Facility Services at Temple University
This capability will further facilitate biomedical research at Temple University by providing expertise in (a) Gene expression data analysis; (b) Management of biological databases and merging with public web resources; (c) Protein structure analysis and functional annotation; (d) Biomedical text analysis.
For ongoing projects with bioinformatics components the core facility will provide free of charge data analysis services as an alternative to outsourcing these tasks outside of Temple or to devoting funds to train lab personnel in this area. Simultaneously, the core facility will provide opportunities to other labs to carry out preliminary bioinformatics data analysis for their grant proposals or articles in preparation.
Gene Expression Data Analysis Services
A team of data analysts will use a combination of commercial products, open source tools, and customized in-house programs to provide basic and advanced gene expression data analysis services. In particular, they will use ImaGene and GeneSight packages; Bioinformatics Matlab Toolbox; Bioconductor open source tools; and TlGR microarray suite. Typical gene expression data management and analysis services provided to Temple investigators will include:
1.
Experimental design support
2.
Platform and scanner independent image analysis and quantification with quality
control
3.
Data management support
4.
Annotation and integration of external biological metadata
5.
Normalization and preprocessing
6.
Basic and advanced data analysis and mining
7.
Visualization and reporting
The core facility will also provide a training support to all interested in using the software independently. This will be achieved by organizing internal tutorials or by providing individual consultations.
Other Bioinformatics Services
1.
Developing an in-house biological database
2.
Developing the core facility web interface
3.
Providing capabilities for protein structure analyses and functional annotation
4.
Providing custom-made bioinformatics solutions for exp1omtory and predictive mining
of biological data
5.
Developing advanced bioinformatics tools for proteome-scale data analysis and biomedical text analysis
RNA sample requirement for ONE slide hybridization
Quantity:
At least 30 μg of high quality of total RNA or 2 μg of polyA RNA in no
more than 10 μl of RNase free water
Quality:
No degradation
No genomic contamination
260/280 ratio> 1.8
Service procedure
1.
Receiving samples
NA samples should be sent in dry ice, at user's expense, to FCCC Microarray Facility during regular business hours, Monday to Friday, 9:00am-5:00pm. The samples can be either sent by expressed mail service or dropped by users
2.
RNA quality control
Microarray facility will run RNA quality control procedure to ensure RNA quality before microarray experiment. If the quality is not meeting the requirement, RNA samples will be returned to user at user's expense or picked up by users
3.
Service turn around time
The microarray hybridization results will be returned to user within 10 business days
4.
Service package
Service package includes RNA labeling, microarray hybridization and slide scanning. Image process and data analysis are not included in the service package and are at user's responsibility to ensure the proper data analysis
5.
The microarray results (Tif. images) will be recorded onto CDs which should be picked up by the users or be sent to the users at user's expense.
6.
FCCC micro array products include
Human 40,000 cDNA (IMAGE clones) arrays: 3 slides (Hu40kI, II and III)
Human 30,000 oligo (SOmers, MWGBiotech) arrays: 2 slides (Hu30kO A and B)
Mouse 15,000 cDNA (NIA15k clones) array: 1 slide
Mouse 32,000 oligo (70mers, Operon) arrays: 2 slides (Mo32kO A and B)
Yeast 6,000 oligo (40mers, MWG Biotech) array: 1 slide
Ordering Procedure:
Call Dr. Li to discuss your experimental strategy (optional)
Use the form below to place your order
E-mail the completed form to John Aybar, jaybar@temple.edu
John Aybar will include the “Master Order Number” and will forward it to Fox Chase
Contact:
Bioinformatics related issues:
Zoran Obradovic, zoran@ist.temple.edu 1-6265
DNA Microarray related issues:
Yuesheng Li, Facility Director ys_li@fccc.edu 215-214-1665 ext. 8426
Invoice, logistics related issues:
John Aybar, jaybar@temple.edu 1-6165
