Fluidigm C1 + RNA-Seq


When combined with RNA-Seq, the Fluidigm C1 provides the ability to analyze the transcriptomes of dozens to hundreds of single-cells.

Microscope access at the University Imaging Center is required to inspect capture efficiency. Users should plan to be on-hand immediately following capture in order to view cells and make go/no-go decision on proceeding with downstream processing.


A 96-cell Fluidigm C1 + RNA-Seq project includes three costs: 1) C1 capture/cDNA creation (on-chip), 2) RNA-Seq library creation (off-chip), and 3) sequencing per se. On the pricing pane, prices for capture/cDNA and library creation are listed (for sequencing, see the Next-generation Sequencing section).


An 800-cell Fluidigm C1 RNA-Seq project includes two costs: 1) C1 capture/cDNA/RNA-Seq library creation (on chip), and 2) sequencing per se (for sequencing, see the Next-generation Sequencing section). On the Pricing pane, prices for capture/cDNA/library creation is listed (for sequencing, Next-generation Sequencing section).


Contact us at single-cell@umn.edu


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Service Scale Unit UMN
Single-chip Capture/cDNA Creation.      
Up to 96 cells. Rate includes: capture chip and reagents, cDNA conversion reagents (Clontech SMARTer) and instrument/labor costs. 1-any run $1,993.53
Single-cell RNA-Seq Library Creation.      
Library creation from cDNA utilizes Illumina Nextera technology, optimized for low-cost, quarter-scale reactions. 1-23
UIC Microscope Access.      
UIC Microscope Access (per 1/2 hour) is charged to all C1 captures and is used to determine capture efficiency. 1-any 1/2 hour $17.67
Single-chip Capture + 3’ RNA-Seq Library Creation.      
Up to 800 cells. Service includes: capture chip and all reagents for cDNA creation and 3’ RNA-Seq library creation. 1-any run $4,464.29

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How to Order

Contact us at single-cell@umn.edu to schedule a capture time. Client needs to be present during scheduled capture time in 1-210 Cancer & Cardiovascular Research Building.

Complete the C1 Project Initiation Form.


Bring 250 cell / uL in a minimum 20 uL media. Single-cell suspension can be submitted in any type of media. Note: Please provide extra media in case the single-cell suspension needs to be diluted.


Captured cells.

An Excel report is emailed to client with PicoGreen concentrations with a link to images in the Imaging Center.