The Microarray Core Facility is a component of the UAlbany Center for Functional Genomics and was established to provide the infrastructure to enable the development of major projects that utilize DNA microarrays for large scale analysis of gene expression. The DNA Microarray Center currently has the ability to run microarrays from various vendors (Affymetrix GeneChip and Agilent Sureselect) as well as others that have been developed by academia or other organizations on a standard slide format. We offer microarray services to probe gene expression, gene regulation, exon splicing as well as epigenetics. The Core also provides instrumentation for scanning of protein arrays (cytokines, antibodies) that were developed on the standard slide format.

The NextGen Sequencing core was established in 2013 and currently houses the Illumina NextSeq 2000 and Oxford Nanopore MinION platforms for next generation sequencing. The core currently offers services in RNA sequencing, ChIP-seq, ChIRP-seq, metagenomics and miRNA sequencing

The Microarray & NextGen sequencing Core also provides bioinformatics tools for further analysis of the results of microarray and sequencing experiments.

Affymetrix GeneChip Analysis

Affymetrix´s proprietary GeneChip technology utilizes photolithography based in–situ synthesis of arrays containing 25–mer oligonucleotide probes. We provide gene expression (3´–IVT, Gene ST and Transcriptome arrays), gene regulation (Tiling) and miRNA on the GeneChip cartridge platform. The core is experienced in working with small samples (LCM, biopsies, FFPE tissue, flow sorted cells and immunoprecipitated material)

Agilent microarray Analysis

Agilent´s proprietary SurePrint technology uses an inkjet, non–contact printing process to produce glass arrays containing 60–mer oligonucleotide probes. We provide gene expression (custom or whole genome), gene regulation (Promoter Tiling), miRNA, epigenetic profiling (DNA Methylation) on the Agilent platform. The core is experienced in working with small samples (LCM, biopsies, flow sorted cells and immunoprecipitated material).

Custom Microarray Analysis

The core can also provide services on any custom arrays supplied by the end user. We have used many such slides spotted at other institutions for 1– or 2–color microarray analysis. Protein or cytokine arrays have also been scanned at our facility.

Superarray Analysis

The core can provide services on qPCR arrays provided by SABiosciences/Qiagen.

RNA/DNA isolation and Quality Control

We can isolate total RNA, mRNA, small RNA, immunoprecipitated RNA and genomic DNA from a wide variety of samples including cell lines, eukaryotic tissues, prokaryotic cultures and plants. We also offer RNA, small RNA and DNA assays on the Agilent Bioanalyzer in order to check the integrity of your sample.

Data Mining Services

The Core Facility offers data mining services for NGS and microarray data using various statistical pipelines incorporating R packages such as DESeq2, CellRanger, Seurat and Transcriptome Analysis Console (GeneChip assays).

Validation of expression analysis data

The facility offers a myriad of services for validation of gene expression data including SYBR Green and Taqman quantitative PCR assays.

Director, DNA Microarray Core Facilty
Sridar V. Chittur
Sridar V. Chittur
Research Associate Professor

Pricing and Forms

The core offers services ranging from nucleic acid isolation or quality check to full microarray or NGS sequencing. The processing charge depends on the level of experimental need. Please contact the core director for a quote tailored to your needs.

Microarray & NGS Sample Submission

Services and Pricing
Premier ServiceUAlbany Academic Price §
RNA isolation to data acquisitionVaries depending on type of array


Full ServiceUAlbany Academic Price §
Total RNA processing#, hyb & scan (3’IVT arrays)$350/sample
Total RNA processing#, hyb & scan (Gene ST arrays)$350/sample
Total RNA processing#, hyb & scan (Transcriptome arrays)$365/sample
Total RNA processing, hyb & scan (miRNA arrays)$240/sample

Prices based on standard Affymetrix protocols. Contact us for pricing if you have small samples, FFPE sample or if your samples require any special processing


NextGen Sequencing ServicesUAlbany Academic Price §
Next Gen Sequencing Prices 


Custom ServicesUAlbany Academic Price §
RNA isolation from tissue$60/sample
RNA nano BioAnalyzer QC (up to 12 samples)$75/chip
RNA pico BioAnalyzer QC (up to 11 samples)$75/chip
DNA high sensitivity BioAnalyzer QC (up to 11 samples/chip)$75/chip
Hybridization & scan only (previously labeled samplefor GeneChip)$100/sample
Hybridization only (previously labeled sample for slide arrays)$100/slide
Data analysis only$75/hr

Prices subject to change and do not include cost of GeneChip arrays.
GeneChips can be purchased from CFG or directly from Affymetrix
GeneChip Arrays should be provided by user at time of sample submission


Microarray and NextGen Sequencing service forms available for download in Adobe Acrobat PDF Format:

Customer Information Form

Microarray Forms

Microarray RNA Submission Form

NextGen Sequencing Forms

Next Gen Sequencing Submission Form


Microarray & NGS: Instrumentation

The Microarray Core is well equipped for detailed studies on gene expression as well as related services including RNA isolation and quality control; hybridizations to Affymetrix GeneChip and in house spotted cDNA arrays.

The Next generation Sequencing core is equipped to carry out studies involving DNA and RNA sequencing for gene expression, gene regulation (Chip-Seq) and metagenomics. The facility houses instrumentation for fragmentation, QC and size separation of DNA/RNA fragments.

Major instrumentation at our core facility include the following:

NextSeq 2000

The NextSeq 2000 desktop sequencing system provides the flexible power and simplicity you need to analyze whole genomes, exomes, and transcriptomes. The NextSeq 2000 Sequencing System leverages the latest evolution of Illumina sequencing by synthesis (SBS) technology, two-channel SBS, enabling a breakthrough reduction in data generation times. Unlike the older four-channel methods, two-channel SBS technology requires only two images to determine all four base calls. This results in a two-fold reduction in image acquisition, reducing cycle and data processing times, while delivering the same high quality and accuracy. The method virtually eliminates errors and missed calls associated with strings of repeated nucleotides (homopolymers).

View most frequently requested applications and the kits used to generate libraries.

Check out the NextSeq 2000 instrument specifications.

Oxford Nanopore MinION

Custom services for gene expression analysis using the Affymetrix GeneChip technology are currently offered at our microarray facility. Instrumentation for Agilent arrays and two-color experiments using custom made cDNA-based arrays is also available.

View most frequently requested applications and the kits used to generate libraries.

Affymetrix GeneChip Fluidics station 450

The fluidics stations automate the washing and staining aspects of the sample processing workflow

Affymetrix GeneChip Scanner 3000 7G

The 30007G scanner allows for high resolution scanning of GeneChips down to 0.51 µm, improving efficiency in genetic analysis for gene expression and DNA analysis applications, including the ParAllele MIP technology. The Autoloader allows temperature controlled handling of up to 48 GeneChips per run.

Agilent BioAnalyzer

The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA, RNA and proteins required in many workflows, including next generation sequencing, gene expression, and proteomics. The instrument utilizes 1 µl of sample for capillary electrophoretic separation and enable fluorimetric quantitation as well as degradation analysis of nucleic acid samples.
Quality metrics such as 28S/18S ratio and RIN (RNA integrity number) are generated also.


The Bioruptor® NGS is the perfect tool for NGS library preparation. This cutting-edge sonication device is dedicated exclusively to DNA shearing and provides suitable DNA for unbiased library preparation prior to next generation sequencing. You will obtain your fragmented DNA up to five times faster than with other standard fragmentation devices.

Axon Genepix Scanner 4000B

This scanner is used to scan Nimblegen and other arrays spotted in a 1" x 3" format at 5 µm -100 µm resolution (16-bit dynamic range). The scanner has 532 nm and 635 nm excitation lasers with emission filters optimized for Cy3 and Cy5.

Agilent DNA Microarray Scanner G2565CA

This high resolution scanner allows us to scan microarrays at 2, 5 or 10 microns. This high throughput scanner can scan the new high density (>1M probes) from Agilent and Nimblegen. The scanner has 532 nm and 635 nm excitation lasers with emission filters optimized for Cy3 & Cy5 and Alexa 647, 555, and 660.

NanoDrop ND-1000

The NanoDrop ND-1000 is a "cuvette-less" spectrophotometer. One microliter of sample is placed on the pedestal and the Nanodrop stretches the liquid into a column of fixed length.
Fiberoptics is employed to pass filtered light through the stretched column. Absorbance at various wavelengths is measured and reported through an attached computer.

Qubit® 2.0 Fluorometer

The Qubit® 2.0 Fluorometer quantitates DNA, RNA, and protein with unprecedented accuracy, sensitivity, and simplicity. It is designed for molecular biology labs that work with precious samples that are rare or difficult to process, and applications requiring precise measurement such as real-time PCR.

Affymetrix Hybridization Oven 640

This high capacity oven is used to incubate the GeneChip cartridge arrays for overnight hybridizations.

Agilent hybridization oven

This rotisserie oven holds the specialized clamps used for Agilent slide arrays.