Deep Sequencing & Microarray Core


Updates to Core services:

Effective 2/28/2018, sample QC will be performed on the Advanced Analytical Fragment Analyzer by default.  Any requests to have samples run on the Agilent Bioanalyzer must be indicated in iLabs and when signing projects in to the lab queue.  For Bioanalyzer requests, please select OTHER as QC type and specify request in Notes section.


Overview of Services

Our aim is to provide 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 and has supported research projects for more than 467 principle investigators, 1097 individual researchers, and processed more than 36,000 samples (as tallied in April, 2016). We offer sample preparation and analysis using Next Generation & Third Generation sequencing technologies, Microarrays, Nanostring nCounter, and qPCR.  We also offer high throughput DNA, Chromatin and RNA shearing using Covaris E220 system. Our lab is equiped with both PacBio and Oxford Nanopore platforms for third generation, long read, single-molecule real-time (SMRT) sequencing, as well as the Illumina NextSeq 500 and MiSeq next-generation sequencer for short reads. We work closely with the GRCF to enable our clients access to the Illumina HiSeq 2500/3000 and NovaSeq for deeper sequencing requirements. The third generation long read sequencing technologies are great for genome assembly, novel transcript isoform identification, full length 16s rRNA gene sequencing for metagenomics, repeat sequence and GC-rich region targeted resequencing, as well as for bacterial DNA methylation study.  The Illumina short read sequencing technology, with its high throughput, is great for whole genome resequencing, whole exome sequencing, RNAseq, ChIPseq, 16s rRNA gene or whole genome metagenomic sequencing, and targeted DNA resequencing.  We run the Affymetrix microarray system, while offering preparation and support for Agilent arrays as well. In addition, we offer the Nanostring nCounter system for RNA expression, FFPE analysis, CNV, and miRNA detection. We ensure a full service experience for our clients, starting with project design, all the way through publication. We encourage our clients to meet with us before beginning any projects to ensure the most accurate and efficient results. From nucleic acid extraction through analysis, we are your one stop shop.  


Core Publications List


Seth Blackshaw, Ph.D. Director
MRB Room 335


Haiping Hao, Ph.D., Associate Director
MRB Room 359
Office Phone: (443) 287-9056
Lab Phone: (443) 287-0262

Location and hours of operation

Hours Location

Hours Open: Monday - Friday 8:30am-5:00pm

Hours Fully Staffed: Monday - Friday 8:30am-5:00pm

733 N Broadway
MRB 360
Baltimore, MD 21205

Links and Resources

1. JHMI Deep Sequencing and Microarray Core

Price list

Search available services: View: by category alphabetically
Data Analysis (3)
Microarrays (26)
Nanostring (3)
Nucleic Acid Extraction (7)
PacBio (4)
Quality Control (4)
RT PCR (1)
Scanning (3)
Sequencing (31)
Shearing (4)