Fees are reviewed semi-annually based upon the Harvard Fiscal Year (July 1 - June 30). Billing is performed on a monthly basis.  The current fees have been updated as of 1/1/2020 and approved by HMS Finance.

Billing Form

Example Project Fees:

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

Line Item Price/Unit Units Internal Price External Price
Set up fee per project  $773* 1 $773 $898
Per run fee  $44* 3 $132 $497
Per sample fee  $7 12 $84 $84
Per 1000 cells  $27 72 $1,944 $1,944
Full day effort  $302 3 $905 $905
Library preparation  $150 12 $1,800 $1,800
Total inDrop Fee     $5,638 $6,128

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

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 Price
Per Project  $773  $898


inDrop Services

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

Line Item Internal Price External Price
Per run fee  $44 $166
Per sample fee  $7 $7
Price per 1000 cells*  $27 $27
1/2 day effort (3 or fewer samples)  $151 $151
Full day effort (4-6 samples)  $302 $302

* 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

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  $150
 4  $600
 8  $1,200

Transcript Specific Libraries*

Number of Libraries
(1000-3000 cells/library)
 1  $100
 4  $400
 8  $800

  * users must provide primers for transcript specific amplification

User Prepped Libraries**

Number of Libraries
(1000-3000 cells/library)
 1  $105
 4  $420
 8  $840

** users may prep libraries in our space with our prepared reagents




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 Price
1 mL  $2,960  $3,060
0.5 mL  $1,480  $1,530
0.1 mL  $296  $306

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

Single Cell Sequencing Self Service Training

Our rate for training is $199 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.


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 $225 for at most 2 consultation meetings. External user consultation fee is $349.

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 available 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 using our PPMS calendar.  You will need to request access to the PPMS system to book a run.  Please select the Single Cell Core Group.  Note you will not be able to sign up until you have had your 10x training.

Self Service / 10x Training Services

  Price/Unit Units Internal Price External Price 
10x Run training  $284 1  $284 $406
10x Library training*  $199 2  $398 $398
Per Self service run  $85 1  $85 $105

*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 Price
Set up fee per project  $773  1  $773 $898
Per run (Staff Time & Reagents)  $181  2  $362 $605
Staff time for library preparation (1-16 samples)  $885  1  $701 $701
Library reagents  $17  16  $266 $266
Sample prep QC (1 per 11 samples)  $111  2  $222 $222
Total 10x Example Fee*      $2,324 $2,692

*This is the cost 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.

HASHING: The use of sample "hashing" can greatly reduce the cost of a scRNA-seq experiment using 10x. We are currently developing pricing for hashing. Please contact us if you are interested in this type of experiment.