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.


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 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.

Safety Training: Users who will prepare samples within the core must have a brief safety training prior to working in the lab. This can be arranged ahead of your run date or done upon your arrival. Users who intend to use the Chromium Controller (10x Genomics) or any other instrument by themselves need to be trained on the user’s samples by SCC personnel (for a fee). This should be arranged with SCC ahead of the scheduled run. Access to the Chromium Controller will be provided upon successful completion of the training. SCC will not be responsible for the self-operation of the Chromium Controller, failure and/or any loss of material as a result.

Upcoming services: SCC is working hard to offer the following new services from 2023-

  • Spatial Transcriptomics
  • Spatial Epigenomics
  • Library preparation for long-read sequencing

Please contact us to enquire about further detail.

Technologies and services

The Single Cell Core (SCC) provides the service of making single cell RNA-seq or ATAC-seq libraries or both from (a) user-provided single cell/nuclear suspensions or (b) single nuclear suspensions prepared by SCC from user-provided frozen tissue. In case of (a), cell/nuclear suspensions must be brought over on ice in the recommended buffer and at the specified cell/nuclear density and viability. Alternatively, users may work on SCC bench space to prepare their samples the day of the experiment. In case of (b), the frozen tissue needs to be sent to SCC in dry ice, at a time agreed upon by both SCC and the USER. SCC will perform optimization to test their standard nuclear prep protocol on one or two non-precious samples to check the quality of the nuclei and will optimize the protocol, if necessary. SCC will send a report of the pilot test to the USER, which will include images of the single nuclei preparation. If the quality is satisfactory for both SCC and the USER, SCC will proceed with the experiment agreed upon by both.

The SCC will then use one of the technologies offered by them (please see the list below) to barcode DNA/RNA and prepare sequence-ready libraries (deliverables). The user can then work with any sequencing core to have the libraries sequenced or use SCC’s help to do so. SCC may choose to perform sample (e.g., tissue dissociation) preparation in custom cases.

  • 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)- From FY 2024, SCC will no longer offer inDrops as a service. Please contact us for any further enquiries. 
    • 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)

Please note that the cDNA/libraries will be appropriately stored at the SCC for a year after the completion of the library prep. After this period they will be discarded appropriately. The SCC is not responsible for any biomaterial storage in the long term for the user, especially if not picked up by the user within this time limit and can discard any biomaterials from a run without informing the user post this period. All users are also required to brief the SCC staff regarding any biosafety or health-hazards related to their biomaterial well in advance to their run.