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.

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.
  • 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 (updated 3/21/2017)

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.


Fees for the services provided by SCC have been updated and the new rates will apply to all work on/after March 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 10,000 cells) and RNaseOUT (Life Tech #10777-019, 1 tube per full run day).

Example Project Fees:

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

Line ItemPrice/UnitUnitsPrice
Set up fee per project $6431$643
Per run fee $273$81
Per sample fee $712$84
Per 1000 cells $1336$468
Full day effort $2993$897
Library preparation $14112$1,692
Total InDrop Fee  $3,865

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 10,000 cells) and RNaseOUT (Life Tech #10777-019, 1 tube per full run day). In the above example, the user will bring 4 tubes of Superscript III and 3 tubes of RNaseOUT.


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

Volume of HydrogelPrice (HMS Quad)Price (with F&A)
1 mL $2,659 $2,791
0.5 mL $1,330 $1,396
0.1 mL $266 $279


Project set up fee

Each project, other than hydrogel purchase, will have a one-time fee to cover administrative services, consultion and advice, as well as follow up project support. Different experimental questions will be defined as separate projects for billing purposes.

Project set up feePrice (HMS Quad) Price (with F&A)
Per experimental question $643 $960


InDrop Services

Per run fee $27
Per sample fee $7
Price per 1000 cells $13
1/2 day effort (3 or fewer samples) $150
Full day effort (4-6 samples) $299


Library Preparation

The 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 $141
 4 $564
 8 $1,128


Alex Ratner
Single Cell Specialist

Sarah Boswell, Ph.D.
Single Cell Senior Advisor

Mandovi Chatterjee, Ph.D.
Single Cell Core Post-Doctoral Fellow


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.]