Fees are reviewed semi-annually based upon the Harvard Fiscal Year (July 1 - June 30). Billing is performed on a monthly basis.  The listed fees have been updated as of 3/1/2021 and are awaiting approval by HMS Finance.

The SCC does not off a single charge per sample service. Due to the variety of services we offer and different project designs there is a lot of variation in price per project. Below are common examples.

Billing Form

Example Project Fees:

Example inDrops Project: 12 samples at 6,000 cells/sample for a quad based faculty member*

Line Item Price/Unit Units Internal Price External Academic Price*
Set up fee per project  $799 1 $799 $949
Per run fee  $54 3 $162 $447
Per sample fee  $7 12 $84 $84
Per 1000 cells  $27 72 $2,016 $2,016
Full day effort  $302 3 $966 $966
Library preparation  $150 12 $1,884 $2,004
Total inDrop Fee     $5,911 $6,466

*F&A (facilities & administartion) charges added on for these services

Commercial users by an additional 10% over the External Academic Price.

Attention:  These fees do not include sequencing or analysis costs.  The SCC does not provide these services, but can help you coordinate sequencing through some of our area cores.

Sequencing can be done at any of the area core facilities. 

Project set up fee

Each project consists of a set-up fee to cover administrative services, consultation and advice, as well as follow up project support. Different experimental questions will be defined as separate projects for billing purposes. Projects are defined as up to 8 runs or 150,000 cells, whichever is reached first. Additional consultation fees may be added to those projects that require a higher level of advisor support. Users of using our 10x Chromium under our staff assisted model will also pay a setup fee.

Project set up fee Internal Price  External Academic Price
Per Project  $956  $1194


inDrop Services

Please note that inDrops services are no longer available to users outside of Harvard University or Harvard Medical School labs.

Prices for sample encapsulation are custom for every project depending on the number of samples and cells collected.

Line item Price
Per run fee $67
Per sample fee $3
Price per 1000 cells* $34
1/2 day effort (3 or fewer samples) $177
Full day effort (4-6 samples) $354

* Minimum library size is 2000 cells.

Runs that start late and/or run long will be charged for overtime at $40 per hour.


Library Preparation

Please note that inDrops services are no longer available to users outside of Harvard University or Harvard Medical School labs.

The suggested maximum number of cells per library is 3,000 as higher cell numbers increase the rate of duplicate cell barcodes.

The number of cells/sample and number of samples will dictate the number of libraries needed.

Standard Libraries

Number of Libraries
(1000-3000 cells/library)
 1  $178
 4  $712
 8  $1,424

 For Transcript Specific Libraries, cost per library is $147. The users must provide primers for transcript specific amplification.



As available, barcoded hydrogel can be purchased for use on your own inDrop instrument.

Hydrogel is sold at a density of 2 Million barcoded beads per mL.  

Volume of Hydrogel Internal Price External Academic Price
1 mL  $3,033  $3,158
0.5 mL  $1,516.5  $1,579
0.1 mL  $303.3  $315.8

Microfluidic chips may also be purchased at $118 per chip.

Single Cell Sequencing Self Service Training

Our rate for training is $244 per 2 hours of training.  Researchers looking for training on running an inDrop setup, making libraries, or learning how to operate our new 10x Chromium should get in touch with core staff for details. External user training fee is $339.


Single Cell Sequencing Consultation (non-core users)

Researchers using single cell services at other facilities can reach out to the SCC for advice on sample preparation and experimental design. The Chan Bioinformatics core will join in these consultations upon request. The internal consultation fee is $270 for at most 2 consultation meetings.

If you are running staff assisted experiments through the SCC this fee does not apply.


Users are required to purchase their own 10x reagents for use on the Chromium Controller in the SCC. 

Discuss your project with the SCC prior to ordering reagents to ensure proper kit is obtained for your project. 

The SCC offers a variety of options for 10x single cell runs. Users may be trained on the instrument then operate themselves.  Please contact SCC for scheduling your run.

Self Service / 10x Training Services

  Price/Unit Units Internal Price External Academic Price 
10x Run training  $319 1  $319 $414
10x Library training*  $244 2  $488 $678
Per Self service run  $85 1  $85 $135

*Training can take 2-8 hours depending on your level of experience. The training covers a 2h block of time. The exact pricing will depend on your project and how you want to be trained.

NOTE:  Self-service 10x users using do not pay our standard project setup fee, but will need to pay a consultation fee of $225 per project in addition to the fees above.

Staff Assisted 10x Runs

  Price/Unit Units Internal Price External Academic Price
Set up fee per project  $799  1  $799 $949
Staff assisted run fee  $233  2  $466 $656
Per sample ecapsulation fee  $6  16  $96 $96
Staff time for library preparation (1-16 samples)  $747  1  $747 $747
Library reagent fee*  $30.25  16  $484 $644
Total 10x Example Fee      $2,493 $3,092

*The actual library reagent fees structure is more complicated and depends if multiple user libraries are prepped together.  This is a rough estimate for the example presented here.

NOTE - These costs are on top of the user purchased 10x reagents for staff assisted run of 16 samples. This assumes you are running 2 chips of 8 samples each. 

10x projects pay the same setup fee as our inDrops users. This covers the cost of our consultation and admin support.