Single Cell Sequencing

The Single Cell & Transcriptomics Core is on the leading edge of single cell research at Johns Hopkins. We offer three different platforms with the ability to sequence RNA, DNA and protein on a single cell level.

Read more information on Single Cell & Transcriptomics Core services and our iLabs page.

10X Genomics Chromium Controller

The 10X Chromium Controller processes up to 10,000 cells per lane. Cells, RT reagents and barcoded gel beads are mixed to create gel beads in emulsion (GEMs), isolating individual cells with a unique primer.  The RT microreaction adds the cellular barcode, and GEMS are ruptured, creating a pool of barcoded cDNA. Subsequent library prep barcodes individual samples to pool for sequencing. The protocol is available for 3’ and 5’ expression, immune profiling, ATAC and spatial transcriptomics. 

10X Genomics Chromium X

The latest release from 10X Genomics for single cell encapsulation, the Chromium X allows for capture of up to 20,000 cells per lane, with even higher numbers for fixed cells. Methods are available for 3’ and 5’ library prep as well as 3’ fixed cells from human and mouse. This new platform combines the well established 10X methodology with new higher throughput methods to increase cell target number and decreasing doublet rates.

10X Genomics CytAssist

The CytAssist will enable the use of pre-cut FFPE slides for spatial transcriptomics on the 10X Genomics Visium FFPE platform.  Probe based assays are available for human and mouse.


3’ gene expression
3’ gene expression with cell surface protein expression
3’ gene expression multiplexing with cell hashing or multiome

5’ gene expression
5’ gene expression with immune profiling
5’ gene expression with cell surface protein expression

Single cell multiome with ATAC & 3’ gene expression
Single cell multiome with ATAC & 3’ gene expression with MULTIome

Single Cell ATAC

Visium spatial gene expression library prep
Visium spatial FFPE gene expression library prep

Nuclei Isolation

Recommended sequencing depth:
3’ & 5’ expression–50K reads/cell
Cell hashing, MULTIome, CSP barcode–5K reads/cell
ATAC – 25K reads/cell

Recommended protocols:

MissionBio Tapestri

The first and only platform for phenotypic and genotypic single cell analysis from the same cell, the Tapestri allows for barcoding of targeted DNA regions as well as protein identification. Tapestri panels are highly customizable for specific regions and genes of interest to minimize wasted sequence. Each Tapestri chip can capture up to 10,000 cells. Stock and custom panels are available. Custom panels can be designed directly through MissionBio.

DNA Panels | Mission Bio

Parse Biosciences

Parse uses reagent-based barcoding for their highest throughput single cell option. Up to 100,000 cells from up to 48 samples can be barcoded in a single plate. Because the protocol is reagent based, there are fewer restrictions on cell size. In-cell RT reactions use sample-specific barcodes to label each sample. Subsequent in-cell ligation reactions add two additional barcodes, with a fourth barcode added during the library stage. The addition of four barcodes produces over 3 million possible barcode combinations, allowing researchers to distinguish between both cells and samples.

Products | Parse Biosciences