Self Genomic Isolation on the C1

C1 Stitch

Availability: 24 hours, 7 days a week.

Overview:  The Fluidigm C1 is a single cell isolation device which uses an integrated fluidic circuit (IFC) chip to capture each cell's individual genomic content for downstream genomic analysis.

The C1 allows you to prepare single cell templates for mRNA sequencing, DNA sequencing, epigenetics or miRNA expression. This single cell isolator utilizes an optically clear IFC chip which allows you to stain captured cells and examine them by microscopy for viability, surface markers, or reporter genes, as well as confirm there is 1 cell in each capture site.  Upon confirmation of singlet capture efficiency, the C1 lyses the cell and amplifies the targeted genomic content based on chip selection and reagents added, which you will then isolate for your genomic analysis.  The C1 is operated using C1 touchscreen software and is available for all labs to use.

C1 Chip

IFC Chip Selection:  To select the correct chip, you must first verify your cell size.  Next, decide what type of genomic analysis will be performed downstream once the cells are harvested. The available chips can capture cells ranging between 5-25 microns in diameter. 

IFC Chip options below:

C1 Open App IFC:  Create new single cell applications.  For flexibility and designed to capture up to 96 cells that are 5-25 microns in diameter.

C1 Preamp IFC:  Enables targeted gene expression to verify gene signatures defining a cell population.  For use in conjunction with the Biomark system. Could be used to examine microRNA regulating gene expression. Designed to capture up to 96 cells that are 5-25 microns in diameter.

C1 DNA Seq IFC:  Explore cell lineage at the whole genome, whole exome, or targeted loci level. Designed to capture up to 96 cells that are 5-25 microns in diameter.

C1 mRNA Seq IFC:  Designed for absolute quantification or full transcriptome (all mRNA).  Designed to capture up to 96 cells that are 5-25 microns in diameter.

C1 mRNA Seq HT IFC:  Designed for absolute quantification or full transcriptome (all mRNA).  Also allows for on-IFC sample multiplexing resulting in lower library prep costs.  Designed to capture up to 800 cells that are 10-17 microns in diameter.

C1 capture site

Setup & Operation:  Workflow starts with priming the IFC chip for sample transfer preparation. The cells are then loaded onto the chip and 1 cell is delivered into individual reaction chambers and will eject the chip once completed. A microscope will then be required to confirm that one cell is in each capture site. You may use a manual brightfield/fluorescent microscope or we would recommend using the Keyence automated microscope in the IRM Imaging Core. The lysis, transcription, and chemistry reagents will be added to the chip, and will then be placed back into the C1.  The appropriate script will be run and each cell will then be lysed and each cell's genomic content amplified. From there one can harvest the cDNA for qPCR on the Biomark or for library preparation for downstream sequencing analysis.

Training:  All C1 users need to fulfill Basic Training requirements.  Click HERE.

Rates:  Click HERE. 

Scheduling:  Click HERE.

Data Analysis:  No data is generated.  Instrument is a sample preparation device used to isolate single cell genomic templates for downstream analysis.

Reference Info:  Click HERE.