Genomics

In this section you will find information related with all the Genomis platforms currently available at the Parnassus Flow Cytometry Core, these are:

  1. Self Genomic Isolation on the C1
  2. Self Genomic Analysis on the Biomark
  3. Self Genomic Library Prep on the Access Array
  4. Self Genomic Isolation on the Mission Bio Tapestri (coming soon)
  5. Nanostring (coming soon)

 

Self Genomic Isolation on the C1

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.


 

Self Genomic Analysis on the Biomark

More details coming soon.  

Available to use now.  

Contact the following people:

Cassandra Belair at [email protected]

 


Self Genomic Library Prep on the Access Array

More details coming soon.  

Available to use now.  

Contact the following people to inquire availability for next Single Cell Project Office Hours:

Claudia Bispo at [email protected]

 


Self Genomic Isolation on the Mission Bio Tapestri

More details coming soon.  

 


Nanostring

More details coming soon.