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 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 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.

Alternatively, RNA isolated from FFPE can be prepared for hybridization to the 3' Expression arrays using the SensationPlus FFPE Amplification and 3'IVT Labeling Kit (Affymetrix). FFPE RNA isolation services are available.

Whole Transcript (WT) Expression arrays
Preparation of biotin-labeled targets from Total RNA for WT Expression analysis will be performed using the GeneChip Whole Transcript Plus Reagent Kit (Affymetrix).

RNA isolated from FFPE can be prepared for hybridization to the WT Expression arrays using the SensationPlus FFPE Amplification and WT Labeling Kit (Affymetrix). FFPE RNA isolation services are available.

Human Tanscriptome Array
The Human Transcriptome Array (HTA 2.0) is the most comprehensive array for interrogating human transcript isoforms for next generation expression profiling. In addition to gene-level detection, the HTA 2.0 provides the necessary coverage and accuracy required to detect all know human transcript isoforms produced from a gene. The HTA 2.0 design utilizes multiple data sources to ensure the broadest collection of transcript isoforms available. The data sources used to design and annotate the array are RefSeq, Ensembl, UCSC Known Genes, UCSC LincRNA transcripts and Broad Institute - Human Body Map lincRNAs and TUCP (transcripts of uncertain coding potential) catalog.

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 2.0 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 which provides a more complete and accurate picture of gene expression than the 3'-based expression array designs. The small format of the array makes it a cost effective expression profiling solution for new microarray users.

miRNA array
The GeneChip miRNA array provides the most comprehensive miRNA coverage by interrogating 203 different organisms on a single array including human, mouse, rat, rhesus macaque, zebrafish and drosophila. The array includes Sanger miRNA database v20 content and additional small nucleolar RNAs (snoRNAs and scaRNAs). The GeneChip miRNA array is designed to independently interrogate pre-miRNA and mature miRNA in the same experiment. Preparation of the biotin-labeled targets for miRNA expression analysis will be performed using the FlashTag HSR RNA Labeling Kit (Affymetrix). The FlashTag HSR 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 6.0 arrays. All DNA samples submitted for genomic analysis will be subject to quality and quantity assessment.

Genome-Wide Human SNP 6.0 (1M SNP)
Preparation of biotin-labeled targets for the SNP 6.0 genomic mapping arrays will be performed using the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 assay kit..

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 645. 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 nucleic acid analysis services utilizing the Agilent Bioanalyzer 2100. Nucleic acid qualitation and quantification is available on a fee per service basis utilizing the RNA6000 Nano kit, RNA6000 Pico kit, Small RNA kit (for miRNA analysis), DNA1000 kit and High Sensitivity DNA kit. The 2100 Expert 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 for information on sample preparation and delivery.

FFPE RNA Isolation
RNA isolation from formalin fixed paraffin embedded (FFPE) tissue is available for the support of the SensationPlus FFPE Amplification and labeling kits. RNA isolated from FFPE using the Qiagen RNeasy FFPE kit can be amplified and labeled for interrogation with the 3'IVT or Whole Transcript expression arrays.

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.

Last modified: Mar 31, 2014
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