Single Cell Core (SCC) at Harvard Medical School specializes in single cell transcriptomics, epigenomics and multiomics. Our mission of is to provide a custom service to the community based on individual need. The members of the Single Cell Core team consult with researchers to understand their project-specific needs and provide expert guidance, tools and assistance for project completion. They are well-versed on multiple single cell technologies, and participate in custom projects for cutting-edge applications and technology development. In collaboration with other institutes and local core facilities the members of SCC are also involved in educating and training researchers with diverse backgrounds. As one of the first single cell core facilities in the area, the team has extensive experience working with many different tissue types across various organisms using multiple high-throughput single cell technologies.


Upcoming core facility closure: SCC staff will not be available on July 1, 2022 (Friday) and July 4, 2022 (Monday) in observance of Independence Day and a bonus day granted by Harvard Medical School.

inDrops Sequencing on NovaSeq update: Attention!!! illumina has come out with new NovaSeq kits (V1.5). We have seen that inDrop libraries are not sequencing correctly for Index read 2 on these NovaSeq V1.5 kits. V1 NovaSeq kits will sequencing inDrop libraries with no issue. Solution! V1.5 kits will sequence inDrop libraries properly if you use a custom recipe for the NovaSeq settings that sequences the libraries using the grafted primer on the flow cell. BPF, Bauer Core, and DFCI cores are aware of this, but you should remind them if sequencing inDrop libraries that they need to use a custom recipe or V1 kit. If sequencing with any other core please have them contact us for details.

Data analysis software: The Single Cell Core has partnered with the Department of Biomedical Informatics to offer free access to Cellenics, a user-friendly cloud-based platform for the analysis of 10X gennomics and BD Rhapsody single cell RNA-seq data. Sign up here or contact for support.

SCC Rate Updates:  The SCC is in the process of updating its rates. New rates will apply to work performed on or after July 1, 2022.

Updated Cancellation Policy:  The SCC will now require 24h notice for run cancellations. Upon the 2nd last minute cancellation users will be charged the effort fee for the run type.

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

Technologies and services

  • 10x Genomics
    • Single cell and single nuclei RNA-seq (both 3' and 5')
    • Single cell ATAC-seq
    • Single cell multiome (transcriptome and epigenome)
    • Feature barcoding (CITE-seq, hashtagging, MULTI-seq, Cell Plex)
    • Targeted library prep
  • BD Rhapsody
    • Single cell RNA-seq
    • Sample multiplexing by hashtagging-like approach
  • inDrops (for Harvard labs only)
    • Single cell and single nuclei RNA-seq (3' only)
  • Parse Biosciences (SPLiT-seq)
    • Single cell RNA-seq (3' only)
  • Fluent Biosciences (PIP-seq)
    • Single cell RNA-seq (3' only)