Single Cell Core

Single Cell Core (SCC) at Harvard Medical School specializes in single cell transcriptomics, epigenomics and multiomics, and spatial transcriptomics. 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 and spatial 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.

Technologies and services

The Single Cell Core (SCC) provides the service of making single cell and spatial transcriptomic libraries. For single cell, we offer 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' and On-chip-multiplexing)
    • Single cell ATAC-seq
    • Single cell multiome (transcriptome and epigenome)
    • Feature barcoding (CITE-seq, hashtagging, MULTI-seq, Cell Plex)
    • Targeted library prep
    • RNA Flex
  • Parse Biosciences (SPLiT-seq)
    • Single cell RNA-seq (3' only)
  • Fluent Biosciences (PIP-seq)
    • Single cell RNA-seq (3' only)

We expanded our services to include Spatial transcriptomics including (a) Imaging based targeted methods and (b) Transcriptome wide sequencing based methods. We support diverse species, varied tissues and multiple sample types including fresh frozen, FFPE and pre-stained slides. We provide end to end solutions based on the project needs. The technologies we tested in-house and support include:

  • 10x Genomics
    • Visium HD Spatial Gene Expression
  • Complete Genomics
    • STOmics (Stereo-seq)
  • Curio Biosciences
    • Curio_Trekker (Slide_TAG)
  • Vizgen
    • MERSCOPE

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.

Flier2024

Announcements

We have added the following services: 

  • Spatial Transcriptomics- VISIUM HD (10X Genomics), STOmics (Complete Genomics) and MERSCOPE (Vizgen)
  • Library preparation for long-read sequencing

Please contact us to enquire about further detail. 

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 email ccbhelp@hms.harvard.edu for support.

Cancellation Policy:  

The SCC will now require 24h notice for run cancellations. Upon the 2nd cancellation users will be charged the run fee for the run type.

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.