The DNA Microarray Core is a full-service facility providing a quality core service to the investigator with minimal microarray experience at a minimal price. The Core has developed a comprehensive program, which will take the investigator through the microarray process, step-by-step, and give the investigator the requisite experience to analyze and interpret microarray data. We use spotted DNA microarrays exclusively, and currently offer 34k Human and 20k Mouse arrays.

Faculty Director: Brian Seed, Ph.D.
Phone: (617) 726-0078
Fax: (617) 726-0077
Email: microarraycore@molbio.mgh.harvard.edu

Other Staff:

Core Manager: Najib El Messadi
Phone: (617) 726-0087
Fax: (617) 726-0077
Email: najib@molbio.mgh.harvard.edu

Danny Park
Phone: (617) 726-0094
Fax: (617) 726-0077
Email: dpark@ccib.mgh.harvard.edu

Location of Core:

The facility is located at 38 Sidney Street, Suite 100, Cambridge.

The MGH Microarray, Sequencing and Synthesis Cores are located in the Clark building,
room 100, across from the 65 Landsdowne Partners Facility.

Major Equipment:

►3 Perkin Elmer GenTAC Hybridization Stations (36 total slide capability)
►1 Perkin Elmer Scan Array Express high throughput scanners (3 color)
►2 Axon GenePix 4000 Scanners (2 color)
►1 Gene Machines Omnigrid Arrayer (fitted with SMP2 stealth pins)
►1 Applied Biosystems 7300 QRT-PCR cycler
►1 Applied Biosystems 7000 QRT-PCR cycler
►1 Agilent BioAnalyzer (RNA QC)
►1 Beckman Biomek Fx liquid handler
►1 Beckman/Sagian Core System liquid handler

►Total RNA quality control
►cDNA synthesis and target labeling
►Hybridization and data acquisition
►Data normalization
►Web-based microarray analysis software
►Custom microarray fabrication
►High density mouse and human oligonucleotide arrays
►Data analysis and biostatistics consultation
►Tutorials in advanced data analysis
►Database of primer designs for QRT-PCR
►Array-CGH (comparative genomic hybridization)

To access the core, please contact Najib El Messadi at (617) 726-0078 or by email at
microarraycore@molbio.mgh.harvard.edu.

Users of the Microarray Core are encouraged to consult with the Core prior to experimentation.
The purpose of this consultation is to assist users with microarray experimental design in order
to maximize the usefulness, relevance, and validity of their acquired microarray data. Both the
manager of the core, as well as the on-staff bio-statistician will offer guidance and assist users
with the experimental design process.

Prior to consultation, users must consider a series of questions to ensure that the biological
question posed is adequately addressed by the experimental design:

1. What is the aim of the experiment?
2. What are the specific questions being asked?
3. What are the most important comparisons?
4. How will these comparisons be made?
5. What controls are planned?
6. What methods will be used to verify the microarray results?
7. What type of downstream data analysis is appropriate?

With answers to these questions in-hand, the Microarray Core can offer guidance to the user
concerning experimental design, sample replication, and sample size.

1. After consultation, reference and test RNAs will be purified by the user according to
   established total RNA isolation protocols. These protocols have been optimized give
   high-quality total RNA from a variety of tissues and cultured cells.
2. Prior to sample submission, total RNA samples must be purified by RNAeasy
   chromatography (Qiagen).
3. For each labeling reaction, the core requires that each purified RNA sample contain a
   minimum of 10 µg total RNA at a concentration no less than 1.5 µg/µL.
4. A sample submission form must be completed and accompany the total RNA samples.
   The samples must be brought to the Microarray Facility by the experimenter dissolved
   in RNAse free water and frozen on dry ice. [Directions to the Microarray Core]
5. Purified-total RNAs will be subjected to quality-control analysis using an Agilent
   BioAnalyzer. The Core assesses the quality of the sample by measuring the 28S/18S
   rRNA ratio. An rRNA ratio cut-off of 1.3 or greater is required. Total RNAs must be of
   sufficient quality and purity to be accepted by the Core. Due to variability in spectral
   measurements of RNA samples submitted to the Core, concentrations of RNA are
   standardized according to the BioAnalyzer analysis. Please use your own spectral
   measurements as an approximation of concentration when diluting your total RNA
   samples. There is no need to pre-aliquot samples for BioAnalysis.

The MGH Microarray Core has developed a streamlined set of data analysis tools that are
freely available to its users. While the Microarray Core will offer guidance concerning
advanced data analysis, the Core will not perform the analysis. After microarray imaging and
basic analysis, the resulting .tiff and raw-results files will be loaded into BASE. BASE is a
microarray software package installed on our servers accessible to you through its
web interface. It provides data storage, filtering, normalization, some basic statistical tests, and
a means to explore your expression data.

Users of the Microarray Core will need to set up BASE user accounts to retrieve the data and
perform the analysis. It is recommended that new users schedule a training session with the
bioinformaticist to learn BASE (and other software if necessary).

https://dnacore.mgh.harvard.edu/microarray/index.shtml