High Throughput PCR (BioMark HD)

The UNC Center for GI Biology has recognized a growing need for affordable high throughput gene expression analysis. In January 2013 the CGIBD acquired Fluidigm’s BioMark HD technology which uses utilizes thousands of intertwining microfluidic valves and channels on a silicon chip to combine cDNA and qPCR probes. This platform performs qPCR on either 48 or 96 different cDNA samples and can interrogate 48 or 96 genes on each of these samples. With this technology the BioMark instrument is capable of conducting real-time quantitative PCR (qPCR), SNP genotyping, and digital PCR assays in a high-throughput, low volume fluidics chip. Currently, the CGIBD Core will offer qPCR with future implementation of SNP genotyping and digital PCR assays.

The BioMark Dynamic Array chip loads individual samples (cDNA) and individual assay/reagent cocktails (TaqMan probes) separately into wells on opposite sides of a Dynamic Array chip. The integrated fluidics circuit (IFC) controllers push samples and reagents through channels until full; then coordinated releasing and closing of fluidic valves allows mixing of samples and reagents into individual compartments within the silicon chip saving thousands of pipetting steps. Each compartment contains only a few nanoliters total volume of the qPCR reaction. The chips are then loaded onto the BioMark System; undergo 35 thermal cycles in approximately 30 minutes. The 48.48 and 96.96 Dynamic Array chip can simultaneously analyze up to 2,304 or 9,216 reactions, respectively.

High-throughput gene expression analysis can be conducted on cDNA from pooled cells, or tissue samples (such as biopsies), or from single cells. The CGIBD Core facility has collaborated with the UNC flow cytometry core to allow investigators to effieciency sort a single cell into 96-well plates containing lysis buffer for RNA isolation. Once cells are isolated by FACS, the Core will conduct all the downstream components including cDNA synthesis, Specific Target Amplification, and qPCR using TaqMan gene expression assays.

The user can supply TaqMan gene expression assays or the user can choose to purchase TaqMan assays from the Core’s TaqMan library.  The Core also has a probe ‘payback’ system that allows investigators to purchase probes to add to the Core’s probe library.  The PI does not pay for individual TaqMan assays they contribute to the Core when running the Biomark qPCR assay; however, the Core will allow other investigators to use these probes, and the cost for each probe used will be credited back to the contributing PI for their future BioMark services.  This system will allow most investigators to access the Biomark technology, which might otherwise be cost prohibitive. If you are interested in this option, please contact the .  A list of available probe sets can be found here.

Instruments:

Services:

Current Services

TaqMan Gene Expression: Samples and TaqMan assays may be submitted for real-time qPCR on the Dynamic Array chips. These are available in two forms: 48 x 48 and 96 x 96. The 48 x 48 arrays enable testing of 48 samples against 48 TaqMan assays (a total of 2304 reactions). The 96 x 96 arrays enable testing of 96 samples against 96 TaqMan assays (a total of 9216 reactions).

Future Services

Taqman SNP Genotyping: Samples and TaqMan assays may be submitted for SNP genotyping on the Dynamic Array chips. These are available in two forms: 48 x 48 and 96 x 96. The 48 x 48 arrays enable testing of 48 samples against 48 TaqMan assays (a total of 2304 reactions). The 96 x 96 arrays enable testing of 96 samples against 96 TaqMan assays (a total of 9216 reactions).

Digital PCR: Samples and either TaqMan probe-based assays or Fluidigm Slingshot reagents may be submitted for Digital PCR analysis on the Digital Array chips. These are available in two forms: 48 x 770 and 12 x 765. The 48 x 770 array will disperse 48 reaction mixes into 770 separate reactions each. The 12 x 765 array will disperse 12 reaction mixes into 765 reactions each.

Pricing:

Service Price
TaqMan Gene Expression – 48×48 $1,400 (2,304 Ct. Values)
TaqMan Gene Expression – 96x96 $2,800 (9,216 Ct. Values)
TaqMan Gene Expression 192x24 ~$2,200 (4,608 Ct. Values)

** Price estimate for standard service including chip, probes, chemistry, and labor.

To place a core use request, click here.

Submitting Samples:

To begin a project using the Fluidigm Biomark System with the core, please contact the to arrange a consultation. Once project details have been coordinate, samples may be submitted.  All samples should be dropped off in Room 030 of the Glaxo Building, and new users are advised to make an appointment to ensure that someone will be available to receive their samples.