Welcome to Johns Hopkins Deep Sequencing & Microarray Core Facility
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.
Our current service portfolio includes the following categories:
-NextGen Sequencing: we offer library constructions, for Illumina HiSeq and MiSeq NextGen sequencing platform; and for various applications: mRNA-seq, ChIP-seq, Single Read, Paired-End Read, Mate-pair, Targeted Resequencing using Agilent Sure-Select Technology,Microbiome 16S rRNA sequencing, and barcode multiplexing. We also offer complete service from library construction, through sequencing, and data analysis.
-Third Gen Sequencing: We offer library preparation, sequencing, and data analysis on PacBio RS Single Molecule Real-Time (SMRT) sequencing platform. Such services includes short circular consensus sequencing for high accuracy for validating SNPs identified using other technologies, for determining mutation linkages, long reads sequencing for identifying potential new transcript isoforms, fusion genes, and chromosomal structure variations, and for helping sequence mapping with short reads especially for sequencing through regions with repetitive sequences. The techonology is also excellent for de nove assembly small genomes, with the new 150K upgrade, a single library and a single smrtcell run can assemble a complete bacteria genome.
-Microarray: We offer multiplatform microarray services including Affymetrix, Agilent, and Roche/Nimblegen. Our instrumentation for microarray analysis include two Affymetrix GeneChip Systems with autoloaders (capable of autoscanning 48 GeneChips each), four fluidic stations, two Affymetrix hybridization ovens, four BioMicro MAUI Hybridization Stations for regular slide microarray hybridization, Axon GenePix Scanner, Agilent′s most advanced 2-Micro Scanner, Agilent hybridization oven and a Robbins Scientific 400 Oven fitted with a rotator for Agilent hybridization chambers. We offer microarray services from all these companies on all their catalog arrays and custom arrays.
-Nanostring: We offer the Nanostring nCounter Analysis services for multiplexed gene expression, miRNA expression, and copy number variation analysis. The nCounter Analysis System utilizes a novel digital technology that use single molecule imaging to direcly counts the molecules without relying on enzymatic amplification. It requires a small amount of samples and offers high level of precision and sensitivity.
-DNA, Chromotin, and RNA shearing: The core offers sample shearing services using either Covaris E210 instrument or Hydroshear 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. The hydroshear is excellent for shearing DNA to a narrow size distribution with peak size larger than 2 kb.
-Data analysis: We offer statistical and bioinformatic data analysis on primary data and downstream functional analyses. We support data from our and other, outside, platforms; and can help with publication and database submission. We also provide commercial software at affordable rates for general use on our workstations or your own machine, either by subscription or by the hour. These software packages include Partek®, Spotfire®, and Ingenuity® Pathway Analysis, and CLC bio® Genomic Workbench and Genomic Server.
In addition, we also offer free pre-experimental consultation to ensure your study to be as successful as it can be, as economical as possible (we KNOW it's expensive!) and most importantly, as scientifically rewarding as possible.
All data generated from the core are stored in a confidential database and are accessible through core ftp server. Data and information supplied by the Core are intended for research use only. This facility is not certified to supply data to be used in clinical care.
The JHMI Deep Sequencing and Microarray Core Facility is located on 3rd floor of Miller Research Building (MRB), formerly known as Broadway Research Building (BRB), in Room 351, and the lab in Room 360, just across the hallway. The core has been in operation since 2002 and has supported research projects from more than 200 principle investigators and 300 individual researchers. The core was initially funded by support from
- The School of Medicine Office of the Dean
- Institute of Cell Engineering (ICE)
- Institute of Basic Biomedical Sciences (IBBS)
- McKusick-Nathans Institute of Genetic Medicine (IGM)
with startup funds, space, and personnel. Currently, the core is operating under a cost-recovery basis and it is our goal to keep user fees as low as possible in order to encourage the utilization of the core by the Hopkins and regional research community.
- Feb. 5, 2016
We have an Illumina NextSeq 500! Today we have received our shipment of NextSeq 500 instrument. This is exciting as the NextSeq 500 can have similar throughput as HiSeq 2500 (comparing to per lane on HiSeq 2500) and the turn around time is just merely one day. This will improve our Illumina sequencing turn around time significantly. Cheers!
- Jan. 8, 2016
Happy New Year! The JHMI Deep Sequencing and Microarray Core would like to take this opportunity to thank everyone for your continued support and business. Last year, the core and our users have had another successful year. By our counting, there have been 28 publications by our users so far, with 10 of them coauthored by core members (see our publication list here). Congratulations to everyone and wish everyone a most successful year in 2016! The core will continue to improve our services and with the new year, more changes is coming. Check back soon for more details!.
We are implementing iLab In the next two month, we will implement iLab lims in our core. Once the implementation completes, we will transition all our requistion process to iLab. Hope that will streamline the process of requesting services from the core.
- Nov. 12, 2015
Our PacBio RS II can run 6 hr movies now (previously four hour movie) and generates >1G data per run!
- Apr. 6, 2015
Due to Illumina price hike, we are adjusting our price related to illumina sequencing and the new price is effective immediately.
- Sept. 26, 2014
PacBio RS II sequencing price increase After reviewing the cost recovery rate for PacBio RS II sequencing services, we have found it necessary to increase the price for our PacBio RS II sequencing services to ensure the sustainability of the service. The new price will take effect immediately for any new project and future adjustment possible if further review indicates the necessity.
- Jun 5, 2014
PacBio SMRTest MICROBE GRANT PROGRAM For your information, PacBio is running a small research grant program that offers upto 4 smrtbell libraries and 8 smrtcell sequencing on microbe (covering all reagents and consumables). Here is a link for you to submit your entry by June 15, 2014.
- Jun. 27, 2013
Core Service Rate Increase For the last few years, we have maintained our rate constant. However due to increased cost for us, we have to institute a rate increase to keep us from loosing money. The new rate is now in our rate schedule and the new rates are effective immediately. The rate increase will not affect projects that is being processed in the core lab, in the core lab queue, or being analyzed in the analysis unit. Any new project will be charged using the new rate.
- Sept. 10, 2012
MiSeq Upgrade. Our MiSeq instrument has been upgraded so that it can now run 2X250 cycle runs and it also doubled the output for 2X150 and 1X50 cycle runs.
- Aug. 30, 2012
Perkin Elmer/Caliper GXII high throughput LabChip system. The JHMI Deep Sequencing and Microarray Core now has a Caliper GXII high throughput LabChip system with abilities to run quality control on hundreds of RNA, DNA, and protein samples.
- July 2, 2012
NanoString $10K reagent grant competition! NanoString has just announced that they are having a grant competition. Please see the flyer for details. We have the nCounter systems in our facility and will be able to provide services on all Nanostring assays including gene expression, miRNA, epigenomics, and copy number variation assay.
- June 7, 2012
Automated Sequencing Library Preparation! We have purchased a Nugen Mondrian SP system thanks to funding from Johns Hopkins Brain Science Institute. The Nugen Mondrian SP System provides an automation solution for sequencing library preparation and offers the ability to generate library from limited amount of DNA (down to 1 ng). This capability opens a whole field of studies that were previously not amenable. Happy Sequencing!.
- May 10, 2012
We have a MiSeq Now! Thanks to Dr. Nancy Craig and HHMI, now the core has an Illumina MiSeq - a fully integrated personal sequencer with a streamlined solution that offers rapid sample prep, push-button fast sequencing and automated data analysis. The MiSeq currently is capable of generating up to 2 Gb of sequence data per run and will soon be able to generate up to 7 Gb of data. It is an excellent option for targeted resequencing, small genome sequencing, RNA sequencing, ChIP sequencing and Methylated sequencing. With single lane and fast chemistry, MiSeq offers a quick turn around from library preparation to sequencing data. For our service rate, please see the rate schedule.
- Mar. 15, 2012
Affymetrix introduces Whole-transcriptome analysis Gene ST arrays for 16 model organisms including Arabidopsis, Bovine, Canine, Chicken, Cynomolgus, Equine, Feline, Marmoset, Medicago, Ovine, Porcine, Rhesus, Rice, Soybean, Zebra Finch, and Zebrafish. For details, please see Model and applied research organisms Gene 1.1 ST Array for details. These arrays are now available in cartridge array format that we can process in our lab.
- Sept. 28,2011
Introducing Affymetrix New Human PrimeView Gene Expression Array: Affymetrix has introduced a new low cost 3 prime gene expression array for research purpose. The new array is called Human PrimeView Gene Expression Array and it covers all confirmed transcribed genes and variants (total 36000 transcripts for gene expression and alternate 3' end of well annotated genes. Please see Affymetrix Web Site for details.
- Aug. 30, 2011
PacBioRS is in the Core: The PacBio RS instrument has arrived in the core. PacBio engineers are working on installing and testing the instrument to have it up and running. For more information on PacBio RS instrument, please visit Pacific Biosciences Company web site. Come back for more update on PacBio RS instrument!
- May 6, 2011
PacBioRS is coming to the core: With the support from School of Medicine Office of the Dean, the core has purchased a PacBio RS third generation single molecule sequencer. The instrument is capable of long read (currently reported read length average 1.5 kb) which will benefit sequencing through repetitive sequences. Other potential application of the instrument include direct detection of DNA methylation and direct RNA sequencing. The expected delivery date of the instrument is late in the summer. Check back to get updated information on PacBio RS sequencer!
- Jul. 20, 2010
Our Core has a new name: To reflect the new service offering and directions the core is taking, we have changed our name to JHMI Deep Sequencing and Microarray Core!
- Jul. 20, 2010
New NanoString nCounter Analysis System: Thanks to a research grant from Johns Hopkins Brain Science Institute, JHMI Deep Sequencing and Microarray Core Facility has acquired a NanoString nCounter Analysis System. The NanoString nCounter Analysis System is the first and only technology platform to deliver highly multiplexed, direct detection and counting of individual molecules in a single reaction without amplification. The first applications for the nCounter Analysis System offer cost-effective ways to easily profile hundreds of gene transcripts, micoRNAs, or genomic copy number variants simultaneously with high sensitivity and precision. This effectively bridges the gap between discovery technologies such as microarrays, and single-plex technologies like real-time PCR. The system includes a fully automated sample Prep Station, a Digital Analyzer, the CodeSet (molecular barcodes) and all reagents needed to perform the analysis. Assay panels are currently available for gene expression analysis, miRNA analysis, and Copy Number Variation analysis. For informations on how to access NanoString nCounter Analysis Systems, please contact us.
- Jul. 8, 2010
NextGen Sequencing Price Online: We have updated our price to include library preparation and Illumina sequencing service fees. Our library preparation service offers low cost (same price as reagent cost from illumina) and high quality results (we have obtained 50 million reads from paired-end sequencing with approximately more than 80% alignable reads). Please contact us to discuss your NextGen sequencing needs.
- Jul. 8, 2010
We have a new server: Thanks to the generosity of Stanley Medical Research Institute, JHMI microarray core now possess a linux based server with dual Quad core processor, 48 GB RAM, and 7.5 terabyte storage space for supporting data analysis on large data sets including nextgen sequencing data.
- Jul. 8, 2010
CLC Genomics Server and Workbench: Thanks to the generosity of CLC Bio, we have installed CLC Genomics Server and CLC Genomics Workbench on a trial basis for analyzing NextGen sequencing data. The Genomics Workbench runs on Macintosh, WIndows and Linux computers, and it imports data from SOLiD, Illumina, 454, and Helicos. Functions in the Workbench include, quality and adapter trimming, de novo assembly, reference assembly, RNA-seq, ChIP-Seq, SNP and DIP detection, and a suite of functionality for microRNA analysis. The Genomics Server allows you to analyze your data with the tools from the Genomics Workbench, but on a remote machine, one with much greater processing power, such as our new server. The Genomics Workbench accesses the Genomics server as a thick client, so you can process your data from your office, but much more efficiently than your desktop computer can. For testing out the CLC Genomics Server or Workbench, please contact Conover Talbot Jr. or Haiping Hao.
- Jul. 8, 2010
New price effective immediately: To ensure that we do not operate at a loss and to reflect our cost changes, we have implemented a price adjustment on Affymetrix arrays. Any new project submitted from July 7, 2010 and forward will be subjected to the new service fees. To minimize the impact of the price change, we have lowered our quantity discount requirement so that projects with 10 or more samples will enjoy a considerable discount as compared to 24 or more samples previously.
- Jan. 1, 2010
Happy New Year from the Core: New Services for the new year - NextGen sequencing, NextGen sequencing library construction, high-throughput sonication using Covaris® E210 instrument.
- May 12, 2009
Hybridization unit new services: Affymetrix Genome-wide human SNP 5.0/6.0
arrays, human mapping 100K and 500K array sets, drug metabolism biomarker panel
DMET Plus array, multiorganism miRNA arrays; Agilent 1 million feature G3
SurePrint Human aCGH arrays.
- May 1, 2009
The monthly charge for using Spotfire has been reduced to $200 per month.
- Feb. 5, 2009
Partek Genomics Suite version 6.4 is available on core workstations in BRB 351.
- Jan. 5, 2009
New pricing/fee schdule for 2009 is available.
- May 1, 2008
New version of Spotfire 9.1.1 is available. Interested users please contact Microarray Core or fill out a account request form.
- March 1, 2008
Partek Genomics Suite is available on the workstations in Room 351 BRB;
- Febuary 1, 2008
Microarray core hybridization unit announces new lower prices for our most popular
array services and new services added to our portfolio.
- November 1, 2007
Microarray Core computer room (BRB 343) has the latest version of Stratagene software installed, ArrayAssist 5.5.1 and PathwaArchitect 3.0.1.
- Ocbober 29, 2007
Welcome Haiping Hao!
Dr. Haiping Hao is the new manager for the Microarray Core Lab.
- October 9, 2007
Analysis Unit institutes a much needed rate hike on Oct 10, 2007 to help meet its costs. The new rate for consultation and analysis requests is $85/hr.
- April 5, 2007
PathArt has been upgraded to 2007 Release 1.Go to JHMI Microarray Core's PathArt Server. (within Hopkins networks only)
- Jan. 16, 2007
PathwayArchect and ArrayAssist Software Packages (from Stratagene) are accessible from Hopkins campuses. Details in the software page;
- Jan. 9, 2007
We are now running PathArt 2006R4. Go to JHMI Microarray Core's PathArt Server. (within Hopkins networks only)
- Aug. 20, 2006
PathArt 2006 R2 is available within Hopkins campuses.
- May 2, 2006
GeneSpring license renewed and license server software upgraded; GeneSpring Users can upgrade to GeneSpring GX 7.3.1;
- June 15, 2005
JHMI Microarray Core has started running its own Spotfire DecisionSite Server version 8.1 . Interested users should refer to the How to download and install Spotfire document for details about its access.
- Dec.16, 2004
Affymetrix announces changes in array production of
older generation of GeneChip®, U95, U34, U74,etc.. See
- Nov. 17, 2004
A new way to access GeneSpring License Server, that will avoid the Mutiple session message that stops GeneSpring running on your desktop. Please read the GeneSpring installation docs for Microsoft Windows or Mac OS X for details.
- May 15, 2004
Hybridization Lab moves to Room 358 BRB. JHMI Microarray Core Facility is in a single location now!
- March 26, 2004
Analysis Unit moves to Room 351, Broadway Reserch Building (BRB).
- Feb. 25, 2004
New requistion form online!
- Feb. 16, 2004
Microarray Core's FTP site launched! Users who have used hybridization unit can download their data. For details please click here or the "FTP server" link on the left menu.
- Jan. 8, 2004 Analysis Unit has moved to Room 527, Broadway Research Building. Most of the services (including Microarray core facility web site and GeneSpring license server) are back to normal.
- Analysis Unit has moved!
Starting 12/16/03, Microarray Core's Analysis Unit is moving from its Jefferson St.Building location to the its temporary quarter located at Broadway Research Building (BRB) room 527.
7/16/03, 9am-12pm - Microarray Core hosts the BioDiscovery "Statistical Analysis of Gene Expression for Microarray Data" seminar.
12/04/02 - Microarray Core hosts the Spotfire for Microarray Data Analysis presentation.
10/28/02 - 10/29/02 - Microarray core presents the BioConductor Workshop for Microarray Data Analysis.
9/3/02 - Analysis Unit starts to offer services on a trial basis
for free! We provide both the access and technical help for some of the most popular packages like
GeneSpring, Spotfire, and Biodiscovery suite (ImaGene and GeneSight) . You can find more details under the software menu on the left.
- 1/30/02 - Official opening Microarray Core
- 1/09/02 - Hybridization Unit initiates service
Last modified: Fri Feb 5 2016