Services Available at the Microarray Facility
We offer centralized access to high density microarray technology for the advancement of research conducted by investigators of KUMC, Kansas Regents Institutions and member institutions of Frontiers: University of Kansas Clinical and Translational Science Institute.
GeneChip expression analysis services provided by the Microarray Facility include Whole Transcript (WT) Expression arrays ( Clariom D arrays, Clariom S arrays, gene arrays and exon arrays), 3' Expression arrays and miRNA arrays. All RNA samples submitted for expression analysis will undergo a mandatory quality and quantity assessment using the Agilent TapeStation 4200.
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 (Life Technologies).
Very low yield total RNA and RNA isolated from FFPE can be prepared for hybridization to the WT Expression arrays using the GeneChip WT Pico Reagent Kit (Life Technologies). FFPE RNA isolation services are available.
Clariom D Arrays
The Clariom D line of WT expression arrays are the most comprehensive array for transcriptome level interrogation of human, mouse or rat for next generation expression profiling. In addition to gene-level detection, the Clariom D provides the necessary coverage and accuracy required to detect all know transcript isoforms produced from a gene. The Clariom D 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 Ensembl, VEGA, NONCODE, lncRNAWiki, UCSC Genes, AceView, miTranscriptome, RefSeq, MGC, MGI, RGD, Concensus CDS, RNA Central, circBase, Human Body Map, lincRNAdb, Publication-specific gene sets and Non-overlapping orthologous mouse gene and transcript models.
Clariom S Arrays
The Clariom S line of WT arrays provide a focused interrogation of gene-level expression across the transcriptome of >20,000 well annotated genes. The data sources used to design and annotate the array are Ensembl, VEGA, NONCODE, lncRNAWiki, UCSC Genes, AceView, miTranscriptome, RefSeq, MGC, MGI, RGD, Concensus CDS, RNA Central, circBase, Human Body Map, lincRNAdb, Publication-specific gene sets and Non-overlapping orthologous mouse gene and transcript models.
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.
3' Expression arrays
Preparation of the biotin-labeled targets for the 3' Expression analysis will be performed using the GeneChip 3' IVT Plus Reagent Kit (Life Technologies) which utilizes an oligo dT based reverse transcription reaction followed by a T7 promoted in-vitro transcription biotin labeling reaction.
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.
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. A minimum project size of 30 SNP 6.0 arrays is required.
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 Genome-Wide Human SNP Nsp/Sty 6.0 assay kit, 30 rxn.
Microarray Target Labeling Quality Control
For all GeneChip platforms, controls removed during the expression analysis or genomic mapping target preparations will be validated using the Agilent TapeStation 4200. 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 GeneChip Scanner 3000 7G with autoloader. Microarray data will be provided to internal KUMC investigators using the Microarray Data Management System (MDMS). Microarray Data distribution for external investigators will be perform using a secure FTP transfer. Assistance with data analysis can be obtained from the KUMC Bioinformatics Core.
In addition to quality control support for the GeneChip microarray system and Illumina sequence library preparation, the Microarray Facility offers nucleic acid analysis services using the Agilent TapeStation 4200. Nucleic acid qualitation and quantification is available on a per sample basis using the TapeStation for the following ScreenTape applications: RNA, D1000 DNA, High Sensitivity D1000 DNA, High Sensitivity D5000 DNA, Genomic DNA. The TapeStation software provides a RNA Integrity Number (RIN) for RNA ScreenTape applications and a DNA Integrity Number (DIN) for DNA ScreenTape assays. Data generated from the Agilent TapeStation 4200 will be provided by email to investigators in a PDF format.
The Microarray Facility also offers nucleic acid analysis services using the Agilent Bioanalyzer 2100. Nucleic acid qualitation and quantification is available on a fee per service basis utilizing the RNA6000 Pico assay kit with a qualitative assay range of 50 pg/ul - 5000 pg/ul in water. The 2100 Expert operational software provides a RNA Integrity Number (RIN) for RNA samples analyzed with the RNA6000 Pico kit. Data generated from the Agilent Bioanalyzer will be provided by email to investigators in a PDF format.
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 Whole Transcript Pico labeling kit. RNA isolated from FFPE using the Qiagen RNeasy FFPE kit can be amplified and labeled for interrogation with the Whole Transcript expression arrays.
Genomic DNA isolation services are provided on a fee for service basis to support Investigators conducting human mapping projects. DNA isolations will be performed using the QIAamp DNA mini kit.
HMW Genomic DNA HMW Genomic DNA isolation services are provided on a fee for service basis to support Investigators performing DNA sequencing methodologies requiring HMW genomic DNA. The Qiagen MagAttract HMW DNA kit will be used to isolate genomic DNA >50Kb.