The SCC is OPEN and following the guidelines set out in the HMS Coronavirus response If you need to see us at the core please contact us by e-mail to arrange a time. 

10x Chromium encapsulations are available for full service. Self service is also available upon training. Please contact core staff directly if you need self service 10x access and would like to be trained.


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.

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

SCC Rate Updates:  The SCC is in the process of updating our rates. New rates will apply to work performed after 3/1/2021 pending approval from the HMS Finance office.

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. 

BD Rhapsody available for pilot projects! We are looking for pilot users who have low cell numbers (500-1000 cell minimum) or cells that they have had difficulties running with other systems. Contact us if you think your project might be good for our pilot studies.

CITE-seq, Cell Hashing, and 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.

Single Cell Core HMS Workflow

Credits: Dr. Cátia Moutinho