Affymetrix GeneChip® Services
Expression Analysis
Affymetrix GeneChip® expression analysis services provided by the Microarray Facility include 3’ Expression arrays or Whole Transcript (WT) Expression arrays (gene arrays and exon arrays). 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 3’ Expression analysis will be performed using an oligo dT based reverse transcription reaction followed by an 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.
| Exon Arrays (Human , Mouse , Rat) The Exon Arrays allow for "exon-level" analysis and "gene-level" expression analysis on a single array. Multiple probes per exon enable "exon-level" analysis and allow you to distinguish between different isoforms of a gene. With "gene-level" expression analysis, multiple probes on different exons are summarized into an expression value of all transcripts from the same gene. |
| Gene Arrays (Human, Mouse, Rat) Gene 1.0 ST Arrays are the latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Each gene is represented on the array by probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3’-based expression array designs. The small format of the array makes it a cost-effective expression profiling solution for new microarray users. |
Genomic Mapping
Affymetrix GeneChip® SNP mapping service provided by the Microarray Facility utilizes the
500K SNP mapping array set. All DNA samples submitted for expression analysis will undergo a mandatory quality and quantity assessment using the Agilent 2100 Bioanalyzer.
| 500K SNP mapping array set Preparation of biotin-labeled targets for the 500K SNP mapping array set will be performed using the Affymetrix GeneChip® Mapping 250K Assay kit ( Nsp and Sty ). |
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
| Tiling 2.0R array set (human, mouse) Investigators planning studies utilizing the Tiling 2.0R arrays are asked to contact the Microarray Facility. |
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. Expression 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 the quality control support for GeneChip® system, the Microarray Facility also offers RNA analysis services utilizing the Agilent Bioanalyzer 2100. The 2100 Expert (B.02.03) operational software provides a RNA Integrity Number (RIN) for each RNA sample analyzed. RNA qualitation and quantitation is available on a fee per service basis with 12 samples per run capability. 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.
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