Gene Expression Microarray
How do I get started?
Using our extensive experience and expertise, Source BioScience LifeSciences will process your RNA samples efficiently, accurately and economically. For the Affymetrix platform we offer 3 levels of entry giving you the flexibility to process your samples as much or as little in your own lab. You can provide us with total RNA, labelled cRNA or fragmented labelled cRNA. We offer free advice regarding projects and data analysis. Contact us now to confirm pricing and to get a custom proposal of work.
I have a proposal - what do I do next?
You should nominate a Project Leader to be our point of contact regarding your project and contact our microarrays to inform us when you would like to send samples. Please send samples Monday - Wednesday only and include your signed proposal, copy of your purchase order and completed sample annotation form.
How much sample should I send?
This is dependent on which entry level you require:
If sending total RNA:
- For one-cycle processing please send total RNA at a concentration of >50ng/µl in a volume not less than 13µl of DEPC-treated water.
- For two-cycle processing please send total RNA at a concentration of >4ng/µl in a volume not less than 6µl of DEPC-treated water.
If sending labelled cRNA:
- Please send 25µg of purified cRNA at a minimum concentration of 0.7 µg/µl. A sample of the original total RNA (0.1-1µg) that we will use to assess sample integrity.
If sending fragmented labelled cRNA:
- Please send the fragmentation reaction to contain exactly 20µg of fragmented cRNA.
If sending total RNA:
- Please send total RNA at a concentration of >15ng/ul in a volume not less than 15ul of DEPC-treated water.
- To maximise success you should endeavour to supply good quality samples with an OD 260/280 ratio of >1.9
What is good quality RNA?
The nature of the assay means good quality RNA is essential. At Source BioScience LifeSciences we pride ourselves on producing good quality data and have a stringent QC system in place. We ask that all samples have an OD 260/280 ratio of >1.9 and test the quality using the Agilent 2100 bioanalyser system. Intact total RNA is represented by two strong ribosomal peaks with a 28S/18S ratio close to 2.0. Below is a profile of what is considered a good quality RNA sample:
An example of a degraded RNA sample can be seen below. Notice the elevated baseline and decrease in the 28S/18S ratio:
If sending cRNA we expect the profile below. A good cRNA reaction is represented by a smear of products falling between 50 and 3000 bases long.
Further information on Quality Procedures for Gene Expression Microarrays.
What happens if samples fail?
At Source BioScience LifeSciences we appreciate the importance of performing thorough Quality Control steps to ensure you obtain the best data possible. However, occasionally samples fail to produce enough labelled product due to undetectable contaminants. Under such circumstances you may wish to repeat using a fresh sample and would be charged for the processing of the initial part of the experiment again. If failure is due to our processing error, repeats would be conducted free of charge.
How will I receive my data?
Data will be posted onto our ftp site into a private directory which is username and password protected. You will be supplied with this username and password by one of our project scientists which will allow you to download all data onto your personal computer on the same day the microarrays are scanned!
Can I compare data from 2 separate projects?
As long as the same labelling protocol has been used throughout your projects, all data can be compared.
I want to analyse the data myself - how do I get the probe information?
We will supply all the probe information in the form of a text file for the Applied Biosystems arrays. For Affymetrix all probe information can be found through NetAffx
Do you offer any experimental design or data analysis support?
Yes, our scientific consulting service includes a free initial consultation on experiment design and various levels of expression data analysis service.
Please go here for more information.
I still have some questions, who can I speak to?
Please contact us for further information. Our specialist will be more than happy to discuss your requirements in greater detail and can provide you with a custom proposal of work with pricing specific to your project.