Welcome to the Single Cell Core (SCC). Harvard Medical School and the Department of Systems Biology is proud to be offering the inDrops 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.

Join us on December 18th at the next  community breakfast hosted by The Harvard Chan Bioinformatics Core (HBC) on Wednesday, December 18th from 9:00 - 10:30am in Modell 100A at the HMS’ Jeffrey Modell Center for Immunology on the quad 

There is no registration for attending, but seating and food will be available on a first-come-first-served basis. This is a time to get together without computers. We welcome anyone with bioinformatics questions or just an interest in bioinformatics to attend, in addition to other bioinformaticians looking for a community. 

Join us on November 21st at the HMS Research Cores Showcase Poster Session & Reception Thursday, November 21st  3 - 5 PM NRB 3rd floor Rotunda

Is your inDrops project published? Let us know!

Check out our Publications page. Let us know if we should add your publication to our li

The Single Cell Core is hiring a Scientific Director!

Check out the job posting here


The SCC has moved! We relocated just around the corner to ARM 517. We have signs posted in our old space in the Klein lab with directions.

Nuc-Seq is compatible with both 10x and inDrops.

NovaSeq runs of inDrops require that you recieve UN-TRIMMED Fastq files. Adapter trimming seems to be causing some loss of valid reads.

10x Chromium Available By popular demand 10x Genomics Chromium is now an option at the Single Cell Core. We offer 10x Single Cell RNA-Seq or scATAC-Seq either as self-service or staff-assisted. Users need to buy their own reagents and can sign up for time to run themselves once they have received training.  


Policy Regarding Storage of Backup Encapsulated Samples              The SCC policy is to store backup encapsulated cells for about 1 year after your run date. If you need your backup emulsion please come retrieve it from the SCC within a few months of your run. Exceptions may be made if needed for your project, but this needs to be arranged with the SCC.


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