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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 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 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 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 Fragment Analyzer allows for high throughput nucleic acid fragment analysis.  The Core provides quality control services, pre- and post- sample prep.

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 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 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:

  • We offer single cell library preparation from both 10X Genomics and SplitBio. 10X Genomics is the foremost name in single cell sequencing. Library preparation methods are available for 3', 5', VDJ enrichment, and ATACseq protocols, each targeting up to 10,000 cells/sample. Multi-seq and cell-hashing multiplex samples decrease library prep cost, while CITE-seq allows interrogation of both cell surface proteins and mRNA expression. Visium spatial gene expression ties histology and next generation sequencing together, allowing users to map the location of gene expression in tissue sections. Library prep and sequencing are available for Visium samples.

    The MissionBio Tapestri uniquely offers DNA or DNA+Protein single cell sequencing. The Tapestri platform is the world’s first and only single-cell solution that provides genotype and phenotype data from the same cell. Based on a novel two-step microfluidic workflow, the Tapestri platform can access DNA and protein in single cells to give you a true multi-omics picture. Targeted and customizable content enables you to focus your research to your areas of interest.

    SplitBio targets up to 100,000 cells in up to 48 samples using combinatorial barcoding to uniquely tag individual cells. Cell populations are fixed prior to library prep to provide a more flexible alternative to fresh cell library preps.

    Single-cell libraries can be sequenced directly through the Core on the Illumina NovaSeq, Illumina’s most high throughput sequencer providing the lowest cost per base.

    For more information, visit our page on single cell sequencing.

  • We offer library constructions for Illumina NovaSeq, HiSeq, NextSeq and MiSeq NextGen sequencing platform, as well as for various applications: mRNA-seq, ChIP-seq, ATACseq, single cell RNAseq, single cell ATACseq, single cell T-cell/B-cell receptor immune repertoire sequencing, targeted resequencing using Agilent Sure-Select Technology, and Microbiome 16S rRNA sequencing. We also offer complete service from library construction through sequencing and data analysis. NextSeq 500 is our production powerhouse for its yield and short run time.

  • We offer Oxford Nanopore sequencing using MinION. The flow cell yields up to 20Gb data and read length up to 300kbp. The library preparation is comparatively simpler than PacBio library prep, and there is no size selection required. We have used Oxford Nanopore technology for de novo genome assembly for both bacteria and eukaryotic species. Long-read sequencing is ideal for highly repetitive and high GC content regions, genome assembly and full genome sequencing for lower level organisms.

  • We offer Affymetrix microarray services. Our instrumentation for microarray analysis includes an Affymetrix GeneChip System with autoloaders (capable of autoscanning 48 GeneChips each), four fluidic stations and one Affymetrix hybridization ovens.

  • The Core offers sample shearing services using a Covaris E220 instrument. The Covaris instrument uses ultrasonic wave with defined wavelength and adaptive focused acoustics (AFA) technology to efficiently shear DNA, chromatin or RNA to size distributions less than 1.5 kb. Covaris is often used for library construction for short-read sequencing.

  • We offer statistical and bioinformatic data analysis on primary data and downstream functional analyses. We support data from our platforms and external platforms, and we can help with publication and database submission. We also provide commercial software at affordable rates for general use on our workstations or on your machine, either by subscription or by the hour. These software packages include PartekSpotfire and Ingenuity Pathway Analysis.

    In addition, we offer free preexperimental consultation to ensure your study is as successful as it can be, as economical as possible and, most importantly, as scientifically rewarding as possible.

 

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
 
  • Linda D. Orzolek, M.S., Director
    • MRB Room 359
    • Office: 410-502-6658
    • Email: ldorsch2@jhmi.edu
  • Jasmeet Sethi, Ph.D., Research Analyst, Bulk Seq 
    • MRB Room 355
    • Office: 443-287-8852
    • Email: jsethi1@jhmi.edu
  • Tyler J Creamer, Ph.D., Sr. Research Specialist II, Single Cell 
    • MRB Room 363
    • Office: 443-287-9056
    • Email: tcreamer@jhmi.edu
  • Conover Talbot Jr., B.S., Bioinformatician, Core Analysis Unit
    • MRB Room 353
    • Phone: 410-614-0443
    • Email: cct@jhmi.edu
  • Seth Blackshaw, Ph.D., Faculty Director
    • Neuroscience
    • MRB Room 335 
    • Email: sblack@jhmi.edu

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

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