|
|
|
|
Background Information
|
What services are provided by the Genomics Core?
Affymetrix GeneChips:
The Genomics Core provides services for the hybridization, staining and scanning of all types of Affymetrix GeneChips. In most cases, we will help you design your study and select the appropriate sample preparation protocol for your purposes. At this time, you will be assigned a project liaison who will coordinate your study. We will also make every effort to pair you with a highly qualified microarray data analyst. Samples ready for placing into hybridization cocktail are provided to the Core along with required QC data and the desired GeneChips. The samples are then hybridized, stained, scanned, and normalized. When the process is completed, you will receive a notification email and compact disk with your data in text format as well as the raw data files.
Affymetrix Expression GeneChips:
Samples can be prepared for hybridization using standard T7 RNA polymerase in vitro transcription reactions (IVT) from as little as 1 ug of total RNA (minimum final yield 15 µg cRNA per reaction). Small sample preparations using 5-100 ng of total RNA are prepared using the NuGEN Technologies Ovation Biotin system (minimum final yield 2.75 µg sscDNA per reaction). We have found no need to isolate mRNA before beginning sample preparation. Amplified and fragmented samples are submitted to the Core with BioAnalyzer tracings of the total RNA (if possible), cRNA or sscDNA, fragmented cRNA or sscDNA, A260/A280 ratio (in TE preferred) and final concentration as determined by spectrophotometer. In limited cases, we can also prepare cRNA or sscDNA from submitted total RNA for expression studies.
Affymetrix Genotyping GeneChips:
Samples are prepared from 250 ng genomic DNA using standard Affymetrix protocols. Each Genotyping array requires 4 µg of amplified PCR product. DNA is provided to the core ready for adding to hybridization cocktail along with spectrophotometer readings and BioAnalyzer tracings. At this time, the Core is not able to amplify samples from genomic DNA, check back for updates.
Printed Oligo Arrays:
The Genomics Core provides services for the hybridization, washing and scanning of printed oligo arrays. Trained Gladstone Scientists also have the option to scan their own arrays, in which case the Genomics Core will perform the hybridization and washing. You will receive a notification email and compact disk with your raw data files as well as the normalized data.
What must I provide to the core?
Affymetrix GeneChips:
Fragmented cRNA samples and Affymetrix expression arrays of your choice. We have obtained UCSF-wide pricing for all arrays. The current price list We also require you to submit proof of the sample quality, in the form of Agilent 2100 BioAnalyzer tracings, of the total RNA, cRNA and fragmented cRNA. In addition we require that you submit A260/A280 ratios for total RNA and cRNA. All data is submitted electronically to the lab.
Printed Oligo Array:
Cy3 and Cy5 labeled cDNA samples, as well as Agilent 2100 BioAnalyzer tracing or gel picture for each sample. In addition we require that you submit A260/A280 ratios for total RNA. Note that the samples should be labeled on the day of the hybridization, please coordinate this with the Genomics Core.
Completed service request forms are required. The forms can be downloaded from the How To Get Started section. Incomplete forms may result in delays.
Where can I find the protocols?
All current protocols are available for download from the Affymetrix GeneChips and Printed Oligo Microarrays sections. Please consult with the Genomics Core Lab before using these protocols so we can assure that you are using the best protocol for your purposes.
How do I start a project?
To start a new microarray project in collaboration with the Genomics Core, please submit a summary of your project to the Genomics Core, using the Genomics Core Project Form. This form is required for all new studies and is used by the Core to track your study. Please contact Chris Barker to discuss project details.After the initial meeting a member of the lab will be assigned to your study as project liaison and will work directly with your lab to coordinate the project.
How much will it cost to run my study?
Prices for both services and arrays (Affymetrix and printed oligo) can be found in our price list section. The Genomics Core is supported by funding from a variety of sources at Gladstone and UCSF, as a result we have a variety of possible mechanisms to provide discounts on services. Please provide complete information on the Genomics Core Project Form so we can correctly apply discounts to your study.
Will the Genomics Core store my data/samples?
The Genomics Core has limited capacity in terms of data and sample storage. Upon request, we will store your original data and/or samples for up to one year. Please see our Price List for details of charges. All sample materials will be returned to your lab upon completion of each study. Note that these materials are stable for at least 1 year at -80C.
|
|
|
|
|
|
