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:

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NextSeq500

The NextSeq 500 desktop sequencing system provides the flexible power and simplicity you need to analyze whole genomes, exomes, and transcriptomes. The NextSeq 500 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).
Check out the NextSeq500 instrument specifications here: http://www.illumina.com/systems/nextseq-sequencer/performance-specifications.html

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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.

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Affymetrix GeneChip Fluidics station 450

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

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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.

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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.

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Bioruptor®

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.

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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.

Picture of Agilent Microarray Scanner

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.

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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.

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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.

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Affymetrix Hybridization Oven 640

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

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Agilent hybridization oven

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

Contact Information

Core Director

Sridar Chittur, Ph.D., M.B.A.

(518) 591-7215

[email protected]

Laboratory

Marcy Kuentzel, M.S.

(518) 591-7219

[email protected]

 

Andrew Hayden, B.S.

(518) 591-7219

[email protected]