Single Cell Services

The Fluidigm C1 Single-Cell Auto Prep System enables capture of up to 96 individual cells for subsequent analysis by QPCR or RNA-Seq. The instrument is based on innovative microfluidic technology that enables rapid and reliable isolation, processing, and profiling of individual cells for genomic analysis. Using an integrated fluidic circuit (IFC) chip, researchers can extract, reverse transcribe and amplify RNA. Two different IFC chips enable this material to be analyzed on either a Fluidigm Biomark using real time PCR technology or an Illumina HiSeq using ultra high throughput RNA-Seq technology.

View a video of how the technology works here.

At this time the facility does not provide full service for this instrument. All runs are currently self-service following training.

We provide training on the use of the C1 instrument approximately once per month or by appointment, if staffing permits. Please check our current training schedule for more detailed information regarding training.

Once trained, end-users can sign up to use the C1 on a web calendar. It is necessary to purchase all reagents either directly from vendors or from our reagents and supplies stock room in advance of conducting any experiments. In addition, coordinating with a cell sorting facility may be necessary prior to cell capture on the C1. There are currently two types of capture chips available for the C1: Pre-Amp and mRNA-Seq.

Pre-Amp Chip

This chip allows you to capture 96 cells, lyse them and pre-amplify specific loci for QPCR. The QPCR assays may be taqman or any evogreen based assay that is compatible with the Fluidigm Biomark instrument. See workflow figure below.

The BPF has a collaborative relationship with the Children's Hospital Boston Core Facility to send users to their laboratory to use the Biomark System. Please check the Children's Hospital Core Facility's website for more information about Biomark runs. The C1 pre-amp process uses the LifeTech Ambion Single Cell to CT kit for amplifying RNA.

There are currently three PreAmp chips available to capture cells of specific sizes:

  • 5 to 10 micron
  • 10 to 17 micron
  • 17 to 25 micron
For more detailed up to date information about this technology please visit Fluidigm directly

RNA-Seq Chip

This chip allows you to capture 96 cells, lyse, RT and amplify mRNA to generate cDNA for RNA-Seq that can be done on the Illumina HiSeq or MiSeq instruments. See workflow figure below.

The Clontech SMARTer and PCR Advantage2 Kits are used in this procedure. Following cDNA production on the C1, Illumina compatible libraries are generated using the NexteraXT method and kit.

There are currently two RNA-Seq chips available to capture cells of specific sizes:

  • 5 to 10 micron (in development, not yet available)
  • 10 to 17 micron
  • 17 to 25 micron
For more detailed up to date information about this technology please visit Fluidigm directly

The instrument is available 7 days a week (prior training required). Please check our calendar for availability.

Note: You must be a member of the C1 instrument calendar and logged into the BPF website to view and schedule events. You may request to join the C1 group here.

  • Life Technologies Countess
  • Fluidigm C1 Single Cell Autoprep
  • Hamilton StarPlus Liquid Handling Robot
  • MJ Tetrad DNA Engine Thermal Cycler
  • Fluidigm Biomark (in collaboration with Children's Hospital Boston Core Facility)

All samples should meet the following criteria:

  • Median cell size should be within the range of each chip. Cells larger than the chip size range can cause clogging problems and complete chip failure. Cells smaller than the chip size range will simply pass through and will not capture or will result in very low capture efficiency. If you are unsure of your cell size, you may sign up to use the LifeTech Countess within our core to characterize your cells.
  • The number of cells loaded on to the IFC chips may vary but generally you will need 166 to 250K cells / ml in native media. 500 to 750 cells will be pipetted onto the chip in a volume of 5 to 20 µl (only 5 µl will enter the chip).
  • If you plan to use fluorescent markers to identify specific cell types, be sure to confirm in advance that an appropriate microscope resource will be available at the time of your capture experiment. Currently the BPF does not have a microscope within the facility and is dependent on using surrounding imaging resource facilities. The scope we have access to currently can only perform bright field analysis of the chip.

Reagents are available from various vendors as listed below. Each project may vary in price depending on the exact procedures performed and the number of cells successfully captured that are passed on to the QPCR or sequencing process. You are responsible for purchasing and supplying your own reagents in advance of conducting the experiments. The core will only provide pipetman, tubes, pipet tips, micro-titer plates and gloves.

Service
Harvard Internal
Harvard Affiliate/Academic
Commercial
Setup Fee Per Array Run Setup Fee Per Array Run Setup Fee Per Array Run
QPCR PreAmp Chip Experiment $98.16 $43.34 $112.89 $49.84 $127.61 $56.34

Vendor Service Catalog Number Cost
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep Array for Pre-Amp (5-10um) 100-5757 $300
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep Array for Pre-Amp (5-10um) 100-6038 $3000
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep Array for Pre-Amp (10-17um) 100-5479 $300
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep Array for Pre-Amp (10-17um) 100-5480 $3000
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep Array for Pre-Amp (17-25 µm) 100-5758 $300
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep Array for Pre-Amp (17-25 µm) 100-6039 $3000
Required Fluidigm C1 Single-Cell Auto Prep Reagent Kit for PreAmp (960 samples - 10 IFCs) 100-5319 $600
Required Life Technologies / Ambion Single Cell-to-CT Kit (2,400 reactions - 25 IFCs) 4458237 $1174
Optional1 Life Technologies / Invitrogen LIVE/DEAD Viability/Cytotoxicity Kit for mammalian cells L3224 $370
Optional2 Microscope Fee for Capture Review and Cell Identification varies
Required3 Taqman, DELTAgene or otder Assays at 100 µM F+R Primers varies
Required4 Children's Hospital Boston Core BioMark Fees for QPCR Assay Run $550 - $1,050
  1. Live/Dead Assay is not necessary but will allow you to determine which captured cells are viable.
  2. Review of the capture is highly recommended. Without this information it is impossible to know if capture was successful. At a minimum, brightfield review of the capture sites should be performed. In addition, if using the live/dead assay or other biomarker stains, use of an appropriate fluorescent scope will be necessary. If you do not have access to a microscope resource please contact the BPF and we will assist you in finding one.
  3. It will be necessary to add appropriate amplification assays to the chip. Various assay chemistries are compatible with this procedure and costs will vary accordingly. Please contact the BPF if you have questions regarding this portion of the procedure.
  4. In order to perform QPCR, a Fluidigm Biomark instrument run is necessary. The BPF has a collaborative agreement with the Children's Hospital Boston (CHB) Core to allow our C1 users access to this service within their core. Costs for this service vary depending on the number of samples / assays. Please contact the CHB staff if you have further questions about this aspect of the procedure.
Service
Harvard Internal
Harvard Affiliate/Academic
Commercial
Setup Fee Per Array Run Setup Fee Per Array Run Setup Fee Per Array Run
RNA-Seq Chip Experiment $98.16 $43.34 $112.89 $49.84 $127.61 $56.34

Vendor Service Catalog Number Cost
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep IFC for mRNA Seq (5-10um) 100-5759 $700
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep IFC for mRNA Seq (5-10um) 100-6040 $7000
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep Array for mRNA Seq (10-17um) 100-5760 $700
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep Array for mRNA Seq (10-17um) 100-6041 $7000
Required Fluidigm Multipak (1 Chip), C1 Single-Cell Auto Prep Array for mRNA Seq (17-25um) 100-5761 $700
Required Fluidigm Multipak (10 Chips), C1 Single-Cell Auto Prep Array for mRNA Seq (17-25um) 100-6042 $7000
Required Fluidigm C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq (960 samples - 10 IFCs) 100-6201 $600
Required Clontech SMARTer Ultra Low RNA Kit for the Fluidigm C1 System, 2 IFCs 634832 $1050
Required Clontech SMARTer Ultra Low RNA Kit for the Fluidigm C1 System, 10 IFCs 634833 $3800
Optional1 Life Technologies / Invitrogen LIVE/DEAD Viability/Cytotoxicity Kit for mammalian cells L3224 $370
Optional2 Microscope Fee for Capture Review and Cell Identification varies
Optional3 Illumina Nextera XT DNA Sample Preparation Kit (24 Samples) FC-131-1024 $775
Optional4 BPF Illumina 2500 Sequencing Run 2-lanes of 2 X 50bp (~250 million reads)
  1. Live/Dead Assay is not necessary but will allow you to determine which captured cells are viable.
  2. Review of the capture is highly recommended. Without this information it is impossible to know if capture was successful. At a minimum, brightfield review of the capture sites should be performed. In addition, if using the live/dead assay or other biomarker stains, use of an appropriate fluorescent scope will be necessary. If you do not have access to a microscope resource please contact the BPF and we will assist you in finding one.
  3. It will eventually be necessary to produce Illumina compatible sequencing libraries with the cDNA produced on the IFC chip. You may order your own reagents and perform library prep in your lab or you may order library prep through the BPF. If ordering through the BPF, purchasing the Nextera Reagents is not necessary. Please see our NGS library prep section for details on Nextera library prep services.
  4. Sequencing depth and run type will depend on the goal of the research project. In general, a paired-end 2 X 50bp run is sufficient for RNA-Seq and a density of ~1 to 3 million reads per single cell library will suffice. Depending on the capture and library success and project goals, the run type and associated costs may vary. Please contact the BPF staff if you have further questions about this aspect of the procedure.
Service
Harvard Internal
Harvard Affiliate/Academic
Commercial
Setup Fee Per Array Run Setup Fee Per Array Run Setup Fee Per Array Run
DNA WGA Chip Experiment $98.16 $43.34 $112.89 $49.84 $127.61 $56.34

Vendor Service Catalog Number Cost
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (5-10 µm) 100-5762 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (5-10 µm) 100-6043 $8000
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (10-17 µm) 100-5763 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (10-17 µm) 100-6044 $8000
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (17-25 µm) 100-5764 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (17-25 µm) 100-6045 $8000
Required Fluidigm C1 Single-Cell Auto Prep Reagent Kit for DNA Seq 100-7357 $900
Required1 GE Healthcare Life Sciences illustra GenomiPhi V2 DNA Amplification Kit 25-6600-30 $192
Required2 Fluidigm illustra GenomiPhi V2 DNA Amplification Kit 25-6600-31 $532
  1. ~5 chips with tube controls or ~8 chips with no tube controls.
  2. ~22 chips with tube controls or ~30 chips without tube controls.
Service
Harvard Internal
Harvard Affiliate/Academic
Commercial
Setup Fee Per Array Run Setup Fee Per Array Run Setup Fee Per Array Run
DNA TGA Chip Experiment $98.16 $43.34 $112.89 $49.84 $127.61 $56.34

Vendor Service Catalog Number Cost
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (5-10 µm) 100-5762 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (5-10 µm) 100-6043 $8000
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (10-17 µm) 100-5763 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (10-17 µm) 100-6044 $8000
Required Fluidigm C1 Single-Cell Auto Prep IFC for DNA Seq (17-25 µm) 100-5764 $800
Required Fluidigm MULTIPACK, C1 Single-Cell Auto Prep IFC for DNA Seq (17-25 µm) 100-6045 $8000
Required Fluidigm C1 Single-Cell Auto Prep Reagent Kit for DNA Seq 100-7357 $900
Required Fluidigm 20X Access Array Loading Reagent 100-7604 Contact Vendor
Required Fluidigm 1X Access Array Harvest Solution 100-1031 Contact Vendor
Required Fluidigm 1X Access Array Hydration Reagent v2 100-7966 Contact Vendor
Required Fluidigm Access Array Barcode Library for Illumina Sequencers-384 (Single Direction) 100-4876 Contact Vendor
Required Fluidigm Custom uniplex primers ASY-AA Contact Vendor
Required Fluidigm Custom multiplex primers ASY-AAX Contact Vendor
Required Roche FastStart High Fidelity PCR System, dNTPack 04 738 292 001 (500 U) $423
Required Beckman Coulter Agencourt AMPure XP A63880 $305
Optional Agilent Technologies Agilent DNA 1000 Kit 5067-1504 $796

Please contact us at nextgen@genome.med.harvard.edu if you have questions about pricing information for your specific project.

Protocols change frequently for this technology. Please visit the Fluidigm knowledge base for the latest protocols.

The C1 procedure does not directly generate data. Please visit the nextgen sequencing section of the BPF for RNA-Seq data analysis information.

Please contact the Children's Hospital Biomark Core for data analysis information for QPCR

Please contact us at nextgen@genome.med.harvard.edu for more information