If you are interested in the Single Cell Core, please start by completing an application and wait to be contacted by the staff to discuss the scope of your request. 

NOTE the SCC does not provide sequencing or anaysis as a service. 

Free cloud-based data analysis tool:

The SCC is working with a team of bioinformaticians and software developers to develop Cellenics. The platform is designed specifically for biologists. It provides automatic data processing, pre-loaded interactive plots, a point-and-click interface to fully explore your data, together with the option to customise and export publishable-quality figures.

Learn more:

Sign up:

Contact for support:

bcl2fastq Conversion

Klein lab bcl2fastq

Full scRNAseq analysis

Data the SCC collected on both inDrops and 10x instruments is available here:!Synapse:syn17017240/wiki/584708

For full service bioinformatic analysis service we suggest you work with the Chan Bioinformatics Core.

Sample Requirements/Tips

Number of cells: 25,000 – 30,000 at a minimum. 
Cells should be at a density of more than 100,000 cells/ml in at least 150ul.

Viability: Ideally greater than 90%

Buffer conditions: Buffer should NOT contain Mg2+, Ca2+ or EDTA.
Most of users resuspend their cells in PBS (without Mg2+, Ca2+ or EDTA) + BSA (upto 1%)

  • Single-nucleus RNA sequencing can be run with inDrops. Several users perform this routinely.
  • A standard inDrops day encapsulates 6,000 cells per sample for up to 6 samples.
  • Optiprep information
  • CITE-seq / Cell Hashing have succesfully run on both inDrops and 10x.

10x Single-cell sample prep resources

10x Genomics provides a tremendous amount of sample prep protocol advice.  Most of the sample prep requirements for 10x are the same for inDrops.  This is a great resource to use for sample prep optimization.

Useful links:

Sample prep-related:

Index information-related:

There are a variety of scRNA-Seq and scNuc-Seq methods available.

Click here for a search of "single cell dissociation scRNA-Seq"

InDrops Method Publications

Sequencing Guidelines

Most users sequence their libraries on a NextSeq 75 bp run:

Read 1: 61 
Read 2: 14
Index 1: 8
Index 2: 8

It is common to have 70-80% valid reads after filtering for valid cell barcodes.

Sequencing on a their libraries on a NovaSeq 100 bp run:

Read 1: 86 
Read 2: 14
Index 1: 8
Index 2: 8

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.

After several runs of inDrops libraries on the NovaSeq, we have identified that there are sometimes issues with NovaSeq data from using the standard adapter trimming options. The samples are sequencing fine, but inDrop runs on the NovaSeq require that you recieve UN-TRIMMED Fastq files. Adapter trimming seems to be causing some loss of valid reads causing you go only get 6 bp of some of the 8 bp index read as well as issues on Read 1. We have seen that Read 1 sometimes need adapter trimming to map well, but this needs to be done after Fastq generation. Please let us know if you experience any issues on a NovaSeq run so we can help troubleshoot and understand the issues for all inDrops users.

library structure


  • Full day or half day services are available. To qualify as a half day run, you must have 3 or fewer samples and be collecting no more than 15,000 cells in total.
  • Run preparation begins 1 hour in advance of the scheduled time. To avoid reagent and service fees, please notify us of any delays or cancellations at least 2 hours in advance of your start time.
  • If you are more than an hour late for your scheduled run, the SCC staff reserves the right to cancel your run and charge you for the reserved time and reagents used in preparation for your run.
  • The SCC will hold on to backup encapsulated cells for 1 year after your run date. If you need your backup emulsion please retrieve it from the  SCC within a few months of your run.