Description of Available Services

Affymetrix GeneChip® Services

Expression Analysis

     Affymetrix GeneChip® expression analysis services provided by the Microarray Facility include 3’ Expression arrays, Whole Transcript (WT) Expression arrays (gene arrays and exon arrays) and miRNA array. All RNA samples submitted for expression analysis will undergo a mandatory quality and quantity assessment using the Agilent 2100 Bioanalyzer.

3’ Expression arrays

    Preparation of the biotin-labeled targets for the 3’ Expression analysis will be performed using the GeneChip  3’ IVT Express Kit (Affymetrix) which utilizes an oligo dT based reverse transcription reaction followed by a T7 promoted in-vitro transcription biotin labeling reaction.
     For investigators working with very low RNA yields, the Microarray Facility provides an alternate target preparation protocol. The Affymetrix Small Sample Labeling Protocol vII utilizes two rounds of in vitro-transcription amplification to generate the necessary quantity of biotin labeled target to hybridize the appropriate 3’ Expression array. Investigators interested in this methodology are directed to contact the Microarray Facility for further information.

Whole Transcript (WT) Expression arrays

      Preparation of biotin-labeled targets for the WT Expression analysis will be performed using the Affymetrix Whole Transcript (WT) Sense Target Labeling Kit. Ribosomal reduction will be incorporated for the exon array target preparations.

miRNA array

    The GeneChip miRNA array provides the most comprehensive miRNA coverage by interrogating  71 different  organisms on a single array including human, mouse, rat, rhesus macaque, zebrafish and drosophila. The array includes Sanger miRNA database V11 content and additional small nucleolar RNAs (snoRNAs and scaRNAs).
     Preparation of the biotin-labeled targets for miRNA expression analysis will be performed using the  FlashTag™ Biotin RNA Labeling Kit (Genisphere). The  FlashTag™  system employs the 3DNA dendrimer signal amplification technology which is composed of a branched structure of single and double stranded DNA conjugated with ~15 biotin labels.

Genomic Analysis

Genomic Mapping

     Affymetrix GeneChip® SNP mapping service provided by the Microarray Facility utilizes the Genome-Wide Human SNP 5.0 or 6.0 arrays. All DNA samples submitted for genomic analysis will be subject to quality and quantity assessment.

Chip-on-chip

    The gene regulation analysis service provided by the Microarray Facility allows for examination of DNA sequences bound by regulatory proteins, plus identifying sites of histone and DNA modification

For all GeneChip® platforms, controls removed during the expression analysis or genomic mapping target preparations will be reviewed using the Agilent Bioanalyzer 2100. After confirming a successful target preparation, it will be hybridized to the appropriate GeneChip® using the GeneChip® Hybridization Oven 640. Washing and staining of the hybridized chip will be completed using the GeneChip® Fluidics Station 450. Scanning of the chip is conducted using an Affymetrix GeneChip® Scanner 3000 7G with autoloader. Microarray data will be provided to the investigator utilizing the Microarray Data Management System (MDMS). Assistance with data analysis can be obtained from the KUMC Bioinformatics Core.

Agilent Bioanalyzer 2100 Services

         In addition to quality control support of the GeneChip® system, The Microarray Facility also offers RNA analysis services utilizing the Agilent Bioanalyzer 2100.  RNA qualitation and quantitation is available on a fee per service basis utilizing the RNA6000 Nano kit, RNA6000 Pico kit or Small RNA kit (for miRNA analysis).  The 2100 Expert (B.02.03) operational software provides a RNA Integrity Number (RIN) for RNA samples analyzed with the Nano or Pico kit. Data generated from the Agilent Bioanalyzer will be provided by email to investigators in a .pdf format.

Nucleic Acid Isolation Services

RNA
     RNA isolation services are also provided by the Microarray Facility on a fee for service basis. RNA isolations will be performed using the Trizol/Phase Lock Gel protocol or Qiagen RNeasy kit. Please refer to the Submission Guidelines for Nucleic Acid Isolation link, listed below, for information on sample preparation and delivery.

DNA
     DNA isolation services will be available on a fee for service basis to support Investigators conducting human mapping projects. DNA isolations will be performed using the QIAamp DNA mini kit.

The downloadable/printable order form for the offered service can be obtained by clicking on the link below. The order form is a .PDF file which needs to be printed using Adobe Acrobat Reader. This form needs to be completed and submitted with your sample. You will also need to download/view the appropriate guidelines for submission at the links below. If you have any questions please contact the facility directly, Tel. (913) 588-7127, E-mail: cbloomer@kumc.edu, for information regarding microarray analysis or any of our other services.

 

• Microarray Facility - Order form
• Submission Guidelines for Nucleic Acid Isolation
  • Tissue/Cell List
• Guidelines for submitting RNA
• Trizol/Phase Lock Gel Protocol
• Pricing for the Microarray Core
• Microarray Facility publications