Microarrays

The JGL Microarray Service offers three main platform technologies, Affymetrix GeneChips, Agilent Catalog Microarrays and custom array making. These technologies allow the simultaneous expression analysis of defined subsets of genes or whole genomes.

 

Contact :


James hadfield for more information at
jicarrarys@jicgenomelab.co.uk

or phone:

  • +44(0)1603 450830 lab
  • +44(0)1603 450847 office
  • +44 (0)7879 844167 mobile

Pricing :


Coming Soon: Online Sample Submission!

 

 


Affymetrix
The JICGenomeLab Affymetrix service uses the Affymetrix GeneChip platform for genetic analysis. The Affymetrix platform allows users to generate reliable, reproducible genetic data. Affymetrix expression arrays allow you to measure gene expression levels both qualitatively and quantitatively and are available for a wide range of organisms. Affymetrix DNA Analysis products allow you to study DNA variation across the whole genome or in specific regions. Mapping arrays are available for genotyping 1500-100000 geneotypes in a single experiment experiments and Universal Tag arrays allow you to design assays to your region or organism of interest. Resequencing arrays allow analysis of up to 30kb of sequence designed to your requirements. All GeneChip arrays are supported on the same suite of Affymetrix instrumentation and are manufactured using the same photolithographic process.

Affymetrix GeneChips use a single color detection system different to the traditional two-colour “cDNA array” technology. This method allows you to generate and easily compare gene expression data generated at different times and locations. Introducing new data points to experiments is easy and allows complex experiments to be built up over time.


Accessing the service:

Pricing:

Gold Service: RNA to data £650

Silver Service: Processing of Fragmented cRNA £75 plus the cost of your chip

 

Pricing is dependant on the type of array you are using and where you are based. All prices are exclusive of VAT. Contact us for a detailed quote.


Sample Submission Guidlines:

Coming Soon: Online Sample Submission!


Gold Service: RNA to Data-Total RNA minimum 15ug at 1ug/u in DEPC-treated water.
Silver Service: Processing of Fragmented cRNA- 40ul of fragmentation reaction prepared according to the Affymetrix Expression Manual Protocols.

Coming Soon: Download the sample submission form

Affymetrix recommend isolating RNA using the Qiagen RNeasy kits. If you use Trizol or other extraction methods then you must perform a clean-up of your RNA using the Qiagen RNeasy kits before submitting your samples. We routinely request 20ug of total RNA at a minimum concentration of 1ug/ul, in DEPC-treated water. You should provide a gel image of the RNA alongside a marker. 10ug is the recommended amount of starting total RNA required for each GeneChip analysis. We would encourage you to send as much RNA as possible as this will allow us to repeat any failed samples immediately without your having to grow plants and extract RNA again.
Your RNA or cRNA will be analysed on the Agilent BioAnalyser. Any samples that are of poor quality will NOT be used unless you specifically ask us to proceed with analysis; it is recommended in this instance that you supply a new sample.
If sending RNA in the mail pack your samples well in dry ice. Please post only on a Monday or Tuesday to avoid samples being left over the weekend. You should include all required sample information data as requested in consultation with the service provider. Indicate which samples you want run and on which type of array. Also indicate if you require Test3 array analysis for QC procedures (JGL recommends Test3s).

Experimental Design

Include replicates! All experiments should be planned with the help of a qualified and experienced statistician if possible. We recommend that you preapre at least one set of replicate material more than you want to include in the final experiment. If there is a problem with one or more of your samples you have material ready for analysis and will not have to grow new plants or obtain more tissue. Journals are becoming stricter in assessing the statistical interpretations you claim in your papers, if you are asked for more replication you can quickly get this data back to referees.

Your experimental system should be well defined and the approprate controls included. Analysis of your system for genes that you know to be affected using Northern or RT-PCR analysis can save you a lot of money on wasted chips. All experiments should be carried out in triplicate if possible. The Affymetrix GeneChip system is a reliable and robust tool for gene expression monitoring, your greatest source of variation is biological and you should perform biological replicate analysis.

  • Plants: True biological replication means growing your plants under exactly the same conditions at a different time or location. Use of a Controlled Environment Room and defined ecotypes or varieties is recommended.
  • Cell Culture: We recommend that you perform experiments on cultured cells at different times, again following strictly defined protocls will reduce the amount of variation to a minimum.
  • Tumour: Tumour biopsies should be devoid of other material, adjacent tissue types or healthy tissue. Microdissection can help in removing these unwanted contaminants. Cells may also be sorted using FACS.

Sample preparation by the Service Provider:

· RNA sample(s) checked on the Agilent BioAnalyzer to confirm RNA quality.
Good Arabidopsis Total RNA Prep

· cDNA sythesis and cleanup.
· cRNA synthesis, cleanup and QC.

Good cRNA profile......................................................Poor cRNA Profile
· cRNA fragmentation.
· Preparation of hybridisation cocktail.
· Hybridisation to GeneChip arrays.
· Data analysis and QC.


RNA will be cleaned, if necessary, using Qiagen RNeasy columns. cDNA synthesis and cRNA in vitro transcription reactions are not guaranteed. The user must meet the costs associated with repeating failed reactions. The Service Provider will inform you of any failures and subsequent cost implications before proceeding.

Coming Soon: Protocols

Clean-up of RNA

cDNA synthesis

cDNA cleanup

cRNA synthesis

cRNA cleanup

cRNA fragmentation

Hybridsation cocktail set up

Small Sample Labelling Protocol

 

 

Coming Soon: Analysing your Affymetrix Data

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FAQs:

How much does it cost per chip?
£565-819 per sample/per chip see pricing ifno fro more details.

What do I get for my money?
We will process your samples and run them on the arrays you request. You will recieve a DVD with your raw data files and a text file containing the analysed data suitable for import into Genespring or other analysis packages.

Filenames?
We recommend you use your initials and a sample name. You must use standard Windows filename conventions. Do not include any of the following characters: / \>< * ?" | : ;

How much RNA is needed?
Standard: A minimum of 5ug of total RNA for each chip, which has been extracted, or cleaned, using Qiagen RNeasy columns. At a minimum concentration of 1ug/ul. We recmmend that you prepare and send us at least 10-20ug of total RNA, this allows us to perform all QC steps and repeat failed reactions if necessarry. All unsued RNA can be returned for further analysis.

Small Sample Protocol: You can start with as little as ng quantities of total RNA. The protocol uses a two round strategy to amplify the necessarry amount of cRNA for GeneChip analysis. You cannot directly compare data from small sample protocol experiments with those using the standard protocol. If you can produce enough total RNA for the standard protocol this is the one we would recommend.

How long will it take?
About 3-4 weeks from receipt of your samples.

How do I analyse my data?
Your data can be analysed using Affymetrix software, Genespring or Excel. All are available in the Genome centre or on site. For more info contact service provider or Computational Biology.

Do I need replicates?
Yes, triplicate seems to be the most useful and cost effective number of reps but try and get some advice if you are not sure about how your samples may vary biologically. Treat this experiment with as much care as you would any other. Microarrays can be used to detect very small changes in gene expression and are susceptible to differences in the way your samples are handled. Speak to the service provider for more information. See experimental Design.

Who do I contact?
James.hadfield@bbrsc.ac.uk or JICarrays@JICgenomelab.co.uk

Guarantees
The JGL Affymertix Service will process your samples using Affymetrix approved protocols. We use several QC steps to check the integrity of your samples before hybridisation to GeneChip arrays. However the JGL cannot guarantee successful analysis using Affymetrix Genechips, we use standard molecular biology techniques with the same risk of failure that you encounter in the lab. The user must meet the costs associated with repeating failed reactions or chips. You will be informed if any samples fail at any QC step and will be given the option of continuing with analysis, repeating the step or sending a new sample. Genechip arrays that fail after successful Test 3 array analysis may be replaced after consultation with Affymetrix. Genechips, which fail after NO Test3 array analysis has been run, are the responsibility of the user.

The JGL cannot guarantee the results from gene expression analysis.You should perform confirmatory analysis such as Northern blots or RT-PCR on interesting genes.