Frequently Asked Questions (FAQ)
1.What are the facility's hours of operation?
2. Where is the facility located?
3. When can I expect to get my results back?
4. What do I need to provide for a microarray?
5. What do I need to provide to have nucleic acids analyzed
by the Agilent 2100 Bioanalyzer?
6. In what form are the results?
7. What are the costs of the services?
8. How do I pay for use of the facility?
9. Who is eligible to use the facility?
10. Do you have a list of the genes
available for the microarray to be used
?
11. How I could have a list
of the probe sequences for Agilent arrays?
1. What are the facility's hours of operation?
The facility is open Monday through Friday during regular business hours.
2. Where is the facility located?
The facility is located at Suite 301 , 417 N. Caroline Street , Baltimore MD 21231 . A map has been provided on our contact page.
3. When can I expect to get my results back?
If your starting materials are tissue samples or cells with a known quality and are to be used for a small number of microarrays, your data will be ready within a week if requested arrays are in stock. It will take one to two additional weeks if arrays have to be ordered and shipped.
4. What do I need to provide for a microarray?
You can provide tissue, cells, or blood samples for microarray studies. Standard protocol for RNA isolation requires minimum of 10 mgs of tissue or one million cells. W e do have alternative protocols for working with smaller size samples such as sorted cells and microdissected tissues.
For RNA samples, we accept a minimum of 1-2 µg total RNA or 30-60 ng mRNA. The concentrations should be 200 ng/µl or higher for total RNA and 6ng/µl or higher for mRNA. For RNA isolation protocol, we recommend homogenization with Trizol plus RNeasy clean-up for tissues and RNeasy for cells.
For CGH microarray, a minimum of 10µg genomic DNA is required for non-amplification protocol and 200ng for protocol with phi29 amplification.
For CGH microarray, a minimum of 10µg genomic DNA is required for non-amplification protocol and 200ng for protocol with phi29 amplification.
5. What do I need to provide to have nucleic acids analyzed by the Agilent 2100 Bioanalyzer ?
Each RNA sample that you wish to have analyzed on the Bioanalyzer should be in TE solution or RNase-free water at a concentration range of 50-250 ng/µl or 100-500 pg/µl. Label the samples clearly.
6. In what form are the results?
Results provided to microarray users: 1) Sample set-up spread sheet. 2) Diagnostic plots including spatial plots of images and boxplots of data sets. 3) Data readout files in text or excel spreadsheet format. Files include pre-processed, background and normalized data points, and statistics from Agilent® feature extraction software. Other results will be provided upon request. Your results are provided on a CD-ROM.
Consulting or performing of further data analysis and bioinformatics will be provided upon request in close collaboration with the Center’s Infomatics Core. This is an additional service and is fee-based.
7. What are the costs of the services?
The cost for each service can be found on the Microarray Facility's Services Pricing Page .
8. How do I pay for use of the facility?
A form with listed services and charges is given to the user when a microarray service request is made. You need to fill in the form and authorize your request by signature. Make sure that the budget number provided is current. Send the form along with samples to be processed to the facility. The form is held until the data CD-ROM is delivered to you.
9. Who is eligible to use the facility?
The facility serves the Sidney Kimmel Comprehensive Cancer Center and the School of Medicine. Anyone wishing to use the facility outside of Johns Hopkins University , should contact facility manager, Wayne Yu.
10. Do you have a list of genes that are available for the microarray to be used ?
A list of available arrays with links to their gene lists can be found on the Arrays Support page. Use the link https://www.rig.onc.jhmi.edu/m_array/ to search the list for genes of interest.
11 . How I could have a list of the probe sequences for Agilent arrays?
You can either request that the Core Facility send you probe sequence information of arrays used or go to the Agilent® website. A Purchase Order Number is needed for the request, which you can get from the Core Facility.
