Welcome to Johns Hopkins 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 every major commercial NextGen sequencing platform: Illumina Genome Analyzer, Applied Biosystem SOLiD, Roche 454, Helicos, and more; and for various applications: mRNA-seq, ChIP-seq, Single Read, Paired-End Read, Mate-pair, Targeted Resequencing using Agilent Sure-Select Technology etc. We also offer complete service from library construction to sequencing to analysis.

-Microarray: We offer multiplatform microarray services including Affymetrix, Agilent, Roche/Nimblegen and Exiqon. 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, and Agilent hybridization oven. We offer microarray services from all these companies on all their catalog arrays and custom arrays at either low or high density.

-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.

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 Microarray Core Facility is located on 3rd floor of 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.

News

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 details;
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: Mon Feb 8 2010