The Single Cell & Transcriptomics Core

The Fragment Analyzer allows for high throughput nucleic acid fragment analysis.  The Core provides quality control services, pre- and post- sample prep.
The Core provides access to many Illumina short read sequencers, including the NovaSeq 6000, NextSeq 500, MiSeq and iSeq, ensuring services can meet the needs of a wide variety of projects at the lowest cost.
The 10X Chromium Controller generates thousands of single cell nano-reactions to barcode up to 10,000 cells per lane for high throughput single cell analysis.  Each chip can process 8 samples at once, capturing 80,000 in less than 20 minutes.  10X assays are available for 3’, 5’, VDJ, ATAC and multiome analysis.
  • The Fragment Analyzer allows for high throughput nucleic acid fragment analysis. The Core provides quality control services, pre and post sample prep.  

  • The Core provides access to many Illumina short read sequencers, including the NovaSeq 6000, NextSeq 500, MiSeq and iSeq, ensuring services can meet the needs of a wide variety of projects at the lowest cost.

  • The 10X Chromium Controller generates thousands of single cell nano-reactions to barcode up to 10,000 cells per lane for high throughput single cell analysis.  Each chip can process 8 samples at once, capturing 80,000 in less than 20 minutes. 

The Single Cell & Transcriptomics Core provides cost-effective and time-efficient access to cutting-edge genomic technologies and expert assistance with experimental design and data analysis. The Core has been in continuous operation since 2002, has supported research projects for more than 500 principal investigators and has processed more than 50,000 samples

We offer sample preparation and analysis using single cell, next generation and third generation sequencing technologies, microarrays, Nanostring nCounter and qPCR. We offer high throughput DNA, chromatin and RNA shearing using the Covaris E220 system. Our lab is equipped with the Oxford Nanopore platform for third generation, long-read sequencing, as well as the Illumina NextSeq 500, MiSeq and iSeq next generation sequencer for short reads. We work closely with the Experimental and Computational Genomics Core (ECGC) to enable our clients to have access to the Illumina NovaSeq for deeper sequencing requirements. We ensure a full-service experience, from project design through publication, and encourage our clients to meet with us before beginning projects to ensure the most accurate and efficient results. From nucleic acid extraction through analysis, we are your one-stop shop.

Our service portfolio includes the following categories:

The Single Cell & Transcriptomics Core Facility is located on the third floor of the Miller Research Building (MRB), formerly known as the Broadway Research Building, in Room 351, and the lab is in Room 360. The core was initially funded with startup funds, space and personnel from:

  • The School of Medicine Office of the Dean
  • Institute for Cell Engineering
  • Institute for Basic Biomedical Sciences
  • McKusick-Nathans Institute of Genetic Medicine/Department of Genetic Medicine

Currently, the core operates under a cost-recovery basis. Our goal is to keep user fees as low as possible to encourage use of the core by Johns Hopkins and the regional research community. For fees please refer to our list of services

Members/Contact:

The Single Cell & Transcriptomics Core
733 N. Broadway, MRB 360
Baltimore, MD 21205
443-287-0262 

For external customers, please contact the Core directly for available services, technical questions and fees.