Single Cell Core

Located at 200 Longwood Ave. in the Armenise Building, room 561.

Single Cell Core (SCC) Research Application

Welcome to the Single Cell Core (SCC). Harvard Medical School and the Department of Systems Biology is excited to be bringing the single cell sequencing technology from the laboratory of Dr. Allon Klein to the greater scientific community. Projects are initiated on a first come, first serve basis upon receipt of your application. We will do our best to respond to applications within a week to book an initial consultation.


Starting July 1st our rates will go up pending approval by HMS Finance. Our new rates are increased by ~25% due to the incorporation of enzyme costs into our encapsulation fee. Due to our bulk purchase of enzymes this results in a net 5% savings to our users. This means that starting July 1st we no longer require you to bring enzymes for your runs.

We hope you will be happy with this change, please feel free to e-mail if you have any concerns regarding this new policy.

The SCC has a new policy to store backup encapsulated cells for only 1 year after your run date. If you need your backup emulsion please come retrieve it form the SCC within a few months of your run. 

Helpful Information

  • Cells need to be >90% viable in single cell suspension after 30 minute to 1 hour in PBS or other mild solution. It is preferrable that cells are >95% viable.
  • Single-nucleus RNA sequencing can be run with InDrops. Several users perform this routinely.
  • Cells need to be supplied in a minimum of 150 ul at a minimum concentration of 160,000 cells/ml (~ 25,000 cells) per sample.
  • A standard InDrop day encapsulates 3000 cells per sample for up to 6 samples.
  • Optiprep information

 READ ME Documents

Useful Analysis Links

SCC Billing Form

Core Poster (3/24/2017)

SCC Policies

  • Full day or half day services are available. To qualify as a half day run, you must have 3 or fewer samples and be collecting no more than 15,000 cells in total.
  • Run preparation begins 1 hour in advance of the scheduled time. To avoid reagent and service fees, please notify us of any delays or cancellations at least 2 hours in advance of your start time.
  • If you are more than an hour late for your scheduled run, the SCC staff reserves the right to cancel your run and charge you for the reserved time and reagents used in preparation for your run.
  • The SCC will hold on to backup encapsulated cells for 1 year after your run date. If you need your backup emulsion please retrieve it from the  SCC within a few months of your run. 

Fees  Disclaimer

Fees for the services provided by SCC have been updated for Fiscal Year 2018. The new rates will apply to all work on/after July 1, 2017.

Fees are reviewed semi-annually based upon the Harvard Fiscal Year (July 1 - June 30). Our billing system is currently under development. Billing is performed on a monthly basis or bi-monthly basis. 

Superscript III and RNaseOUT are not included in the fee structure. Users are responsible for providing their own Superscript III (Life Tech, #18080044, 1 tube per 20,000 cells) and RNaseOUT (Life Tech #10777-019, 1 tube per 50,000 cells).

Fee Summary

Example Project Fees:

Project: 12 samples at 3,000 cells/sample for a quad based faculty member 

Line Item Price/Unit Units Price
Set up fee per project  $758 1 $758
Per run fee  $31 3 $93
Per sample fee  $7 12 $85
Per 1000 cells  $14 36 $508
Full day effort  $277 3 $832
Library preparation  $150 12 $1,800
Total InDrop Fee     $4,076

Superscript III and RNaseOUT are not included in the above fee structure. Users are responsible for providing their own Superscript III (Life Tech, #18080044, 1 tube per 20,000 cells) and RNaseOUT (Life Tech #10777-019, 1 tube per full run day). In the above example, the user will bring 2 tubes of Superscript III and 1 tubes of RNaseOUT.


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

Volume of Hydrogel Price (HMS Quad) Price (with F&A)
1 mL  $2,916  $3,048
0.5 mL  $1,458  $1,524
0.1 mL  $292  $305


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.

Project set up fee Price (HMS Quad)  Price (with F&A)
Per experimental question  $758  $1,075


InDrop Services

Per run fee  $31
Per sample fee  $7
Price per 1000 cells  $14
1/2 day effort (3 or fewer samples)  $139
Full day effort (4-6 samples)  $277


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.

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

Number of Libraries
(1000-3000 cells/library)
 1  $150
 4  $600
 8  $1,200


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 consultation fee is $200 for up to 2 hours. 

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



Sarah Boswell, Ph.D.
Single Cell Core Director



Mandovi Chatterjee, Ph.D.
SCC Post-Doctoral Fellow


Alex Ratner
Single Cell Specialist

Recent Publications

  • Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW (2015).  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells.  Cell 161, 1187-1201. PMID: 26000487  [A PDF of this paper is available for download.]  


  • Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L (2017). Single-cell barcoding and sequencing using droplet microfluidics. Nat Protoc. Jan;12(1):44-73. PMID: 27929523 [A PDF of this paper is available for download.]