Herbert Irving Comprehensive Cancer Center

      

    

    

      

        

                Flash Section

        

        
HICCC

      

      

      

               
    



        
            

                

                


                    




      				

  

      
Genomics Technologies



    
    
    User Fees & Policies
    
    
    Affymetrix Samples:
    
    
      
        
    • All samples should be prepared as per the Affymetrix protocol.
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    • cRNA for gene expression arrays should be deposited in 1.5 ml tubes containing 15 ug fragmented and labeled cRNA in a maximum 130 ul volume.
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    • cDNA for SNP arrays should be deposited in 1.5 ml tubes as fragmented cDNA in 70 ul volume as per the Affymetrix protocol for SNP samples.
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    Agilent Samples:
    
    
      
        
    • All samples should be prepared as per the Agilent protocol.
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    • The services using the Agilent platform include: 
      
        i) ChIP-chip arrays
      
        ii) Expression arrays
      
        iii) miRNA arrays
      
        iv) CGH arrays
      
        v) DNA arrays
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    Imaging
    
    
    Users who have paid the annual fee per calendar year may use the imaging equipment in the instrument room at ICRC 401A. The equipment is available on a first come, first served basis and filling the signing up sheets is mandatory. The available equipment includes a densitometer, a GE Healthcare Storm 8200 instrument and a GE Healthcare Typhoon Trio.
    
    
    Storm 820 is intended for the scanning/quantitation of radioactive images of gels, Western, Southern, and Northern blots.
    
    
    Typhoon applications include quantitation of ethidium bromide stained gels, high sensitivity nucleic acid and protein detection in gels and blots by chemoluminescence or fluorescence and high throughput nucleic acid quantification in 96 well plates using PicoGreen stain For more information please consult the Typhoon Trio user manual or click here for an abbreviated brochure on the instrument capabilities.
    
    
    Quantitative PCR
    
    
    The facility has PCR machines available for quantitative analysis of nucleic acids.
    
    
    Applied Biosystems 7500 Real-Time PCR System, 96-well plate five-color platform calibrated for FAMTM/SYBR® Green I, VIC®/JOE TM , NED TM/ TAMRA TM / Cy3TM, ROXTM/Texas Red®, and Cy5TM dyes.
    
    
    Applied Biosystems 7500 Fast Real-Time PCR System is similar to the 7500 Real-Time PCR system plus is optimized for fast cycling, delivering results in as little as 30 minutes. Requires Fast optical plates and Fast Universal PCR mastermix.
    
    
    PCR machines require advance scheduling and an account number at the time of the reservation. Click here for scheduling information.
    
    
    Idaho Technologies Light Scanner:
    
    
    The LightScanner system is based on Hi-Res Melting, a post PCR approach for a fast and cost effective solution for re-sequencing and mutation discovery projects. Check http://www.idahotech.com/LightScanner/ for more information and detailed protocols.
    
    
    Lightscanner requires advance scheduling and an account number at the time of the reservation. Click here for scheduling information 
    
    
    Next Generation Sequencing
    
    
    
    For whole genome sequencing, whole exome, RNA-seq, ChIP-seq, and targeted resequencing on Illumina HiSeq, MiSeq and LifeTech IonTorrent, please  nextgen@columbia.edu and see http://genomecenter.columbia.edu/?q=node/14.
    
     
    
    
    
    User Fees
    
    
     
    
    
    Molecular Cytogenics Service
    
    
    Investigators are advised to contact the facility for initial discussions regarding the requirements for cell and tissue specimen preparations to best facilitate the required testing. Technical assistance is also provided for custom design and preparation of probes for FISH.
    
    
    User Fees
    
    
    
        
            
    
                 
                Cancer Center
    
                Member ($)    		
                Non-CC Member ($)
            
    
            
    
                Culturing of tumor cell line and preparation of slides
                75
                150
            
    
            
    
                Establishment of cell culture from rodent tumors
                85
                170
            
    
            
    
                Culture, chromosome preparation, and G-banded 
    
                karyotype of human/rodent tumor cell line    		
                200
                400
            
    
            
    
                Culture, chromosome preparations, G-banded karyotype of rodent tumors
                250
                500
            
    
            
    
                DNA probe labeling and testing
                75
                150
            
    
            
    
                Culture, chromosome preparation and single color FISH analysis
                150
                300
            
    
            
    
                Culture, chromosome preparation, and multi-color FISH analysis
                200
                400
            
    
            
    
                Single Color Paraffin section FISH
                125
                250
            
    
            
    
                Multi-color Paraffin Section FISH
                175
                350
            
    
            
    
                Single color FISH on Tissue array
                350
                700
            
    
            
    
                Multi-color FISH on Tissue array
                400
                800
            
    
            
    
                Culture, chromosome preparation, and SKY on human metaphase cells
                500
                1000
            
    
            
    
                Culture, chromosome preparations, and SKY on mouse metaphase cells
                550
                1100
            
    
            
    
                Preparation of PAC/BAC DNA for FISH testing
                125
                250
            
    
            
    
    
    
     
    



 
  


  

    

        


       
 
  


  
  
  
  


                


                

                

            


	      


  
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