DNA Microarray Center
Duke Microarray Core Facility, home Affymetrix: forms, cost, genelist, protocols spotted Arrays: forms, cost, genelist, protocols RTPCR: docs, forms, cost etc info about BASE: Database for spotted array Publications Analysis Softwares, Links FAQ for our services
Printed Oligonucleotide DNA Analysis
Using a GeneMachines Omnigrid arrayer, the facility has the capacity to generate printed microarrays of various forms.
  • Cost of Services
    Service

    Cost

    Reduced Cost**
    Agilent analysis for RNA quality check alone (no probe development)

    $25

    $25
    Microarray Chip + check RNA quality, label RNAs, hybridization, scan, and analysis

    $300

    $150
    Microarray Chip + hybridization, scan, analysis

    $200

    $100
    Label RNAs, hybridization, scan and analysis

    $200

    $100
    Cost of human, mouse, rat and yeast microarray chip alone

    $150

    $75
    Amplification of RNA (starting greater than 500ng, 1 round), check RNA quality, label RNas, chip, hybridization, scan, analysis

    $420

    $210
    Amplification of RNA (starting less than 500ng, 2 round) check RNA quality, label RNAs, chip, hybridization, scan analysis

    $480

    $240
    Cost of scanning and analysis on Axon GenePix software

    $50/hr

    $25/hr
    Set up fee to transfer print sets from 96 to 384 well plates

    $50

    $25
    Cost per plate for transferring print sets

    $15

    $7.50
    Set up fee to print "lab provided" products

    $100

    $50
    Cost to print 384 plate for up to 100 slides

    $35/plate

    $17.50/plate
    Cost of Duke polylysine slides

    $2/slide

    $1/slide
    Cost of CGAP slides

    $11/slide

    $5.50/slide
    Cost of drosophila microarray chip alone

    $75

    $75

    ** Due to support from NIH and NCI center grants, investigators with funding from the NHLBI, NINDS/NIMH, and members of the Duke Comprehensive Cancer Center, as well as investigators that participate in the Duke environmental genomics center, are eligible for reduced pricing.

  • Available Arrays: PLEASE NOTE: Gene annotation is based on what is provided by Operon or by the supplier of the printing set. Please be aware that NOT ALL oligos are clearly annotated. We will try to update the lists from public databases on a quarterly basis.
    Type Source

    No. Sequences

    List of Genes

    		 GeneSpring Genome File (master gene table)
    Mouse Operon Mouse Oligo Set, version 3.0

    30K

    mouse, v3.0

    		 mouse, v3.0
    Mouse Oligator MEEBO Mouse Genome Set

    39K

    MI39K

    		 MI39K
    Human Operon Human Oligo set, version 3.0 35K human, v3.0 human, v3.0
    Rat Rat Operon 3.0 plus Rat MWG array

    38K

    rat,v3.0 & rat MWG array

    		 rat,v3.0 & rat MWG array
    Rat Rat Operon 3.0

    27K

    rat,v3.0

    		rat,v3.0
    Yeast Operon Yeast Genome Oligo Set

    6K

    yeast

    		 yeast
    Songbird Jarvis Lab cDNA Set

    18K

    songbird

    		 songbird
    Drosophila Operon Oligo Set

    15K

    Drosophila
    miRNA (Human&Mouse) Ambion mirVana miRNA

    200

    miRNA

  • Instructions to install GeneSpring Genome File (for GeneSpring 7.0):
    1. Download genespring genome file from table above. (do right click -> save target as)
    2. click here for GeneSpring's Help on "Importing Tab-delimited Genome Files". Follow the instructions.
      1. in step 6, use the first column as "systematic name" and use the GenBank column as "GenBank Accession Number" (LocusLink as LocusLink). Based on the genespring genome file, select the right option for "Use column title s as annotation names"
      2. We don't have sequence files. so skip (click on "next") for the "Importing Genome Sequences" window.
    3. Call us if you still have trouble to load the Genome file.
    4. After installed the Genome File. You can download all annotations from GeneSpring by: a) open GeneSpring b) select the genome c) go to annotation menu ->gene spider -> update annotations from Silicon Genetics... d) click "start" in the new window. This will take a while.
  • Operon Oligo Genome Set Search
    • Want to know if the genes you interested in are in our arrays or not? Please use the program below. Just select the type of ID you are going to search (GenBank/RefSeq or Operon), then select the array and enter ID Numbers in the input box below (on the left), one per line and press the "Search" button on the bottom. If you want to clear the Input/Output, use the "Clear Input/Output" botton next to the search button.
    • *to run this program, you need Java 2 Platform, Standard Edition, v 1.4.2 (J2SE) installed to your computer. If you don't have it, cllick here for the download site.
    • *to make sure we search all possibilities, please enter both GenBank(EMBL) & RefSeq Numbers for the gene your are interested in.
    • *To save the output into a file: 1. move mouse into the output box, click once. 2.hold Ctrl+A to select all. (or right click the mouse, and use the drop down menu) 3. hold Ctrl+C to copy selected. (or right click the mouse, and use the drop down menu) 4. open a new file (text file, excel, word anything), and do a paste into the new doc. 5. save the file.
  • Technical Note: Comparison spreadsheet of the M017N vs. EPA M017K print runs, controls and differences are highlighted. Comparison of Oligos
  • The Oligo Microarray Database (OMAD) provides information on each probe (e.g., name, length and melting temperature) and its representative open reading frame (ORF) or gene (e.g., name, symbol and description) as well as links to public domain databases.  Also included is potential cross-hybridization (X-Hyb) information based on sequence similarity of the probe to all other known genes or ORFs in the genome. This X-Hyb information can be used to provide a more in-depth analysis of the results of hybridization experiments. http://oligos.qiagen.com/arrays/omad.php

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