How much does it cost per array?
This is dependent on sample number. Please contact us for a quote.
What is the best method to use for extracting your RNA?
We do not recommend a particular method. If you have an established method that gives you good quality RNA please continue to use this. However, please bear in mind that total RNA extraction methods differ in numerous ways and may have an impact on:
- the inclusion of small RNAs in the total RNA extraction
- the quantification of the total RNA
Note: extraction methods that use organic solvents such as TRIZOL may result in inaccurate quantification, because organic solvent contamination from carry-over during the RNA extraction may compress the 260/230 ratio. The affected 260 measurement may result in inaccurate quantification of the total RNA.
For further information please read our RNA purification guide.
What is the best method to use for extracting your miRNA?
For miRNA arrays we require total RNA input so there is no need to isolate small RNAs. As with total RNA we do not recommend a particular method. However, the extraction methods listed below have worked successfully with Agilent’s miRNA Microarray System:
- Qiagen miRNeasy Mini Kit
- Life Technologies – TRIZOL Reagent
When you use these or any other commercial kit, use the total RNA isolation protocol. Do not use the size fractionation or small RNA enrichment protocol. You must use the same total RNA extraction methods to obtain consistent results for comparative experiments. Different total RNA extraction methods may result in slightly different miRNA profiles.
How do I submit my samples?
Please read the sample submission guidelines page. An online sample submission form must be completed before sending your samples. There is a direct link to our online submission portal on our home page.
Should I include replicates?
Microarray experiments should be treated like any other experiment in which you would as a matter of course include replicates. Having insufficient biological replicates will lead to an increase in the false discovery rate. You should also consult with a bioinformatician before conducting your experiments.
What labelling kits does the Ramaciotti Centre use?
The Centre uses reagents, kits and protocols as recommended by Affymetrix or Agilent. If you wish to know more about the protocols used on your particular array type please contact us and we will email you a copy of the full protocol. Alternatively the protocols we use can be found on either the Affymetrix or the Agilent website.
What quality control measures are taken by the Centre?
All samples submitted to the Ramaciotti Centre microarray service must first pass initial quality control (QC) checks. Only samples that pass QC will progress to sample processing. Failed samples will be rejected and $15 charged for consumables and labour. The decision on whether to process a sample remains with the customer. In the case where a poor quality sample is processed, the facility cannot guarantee the outcome and the customer must accept responsibility. Customers can resubmit additional samples to complete their experiment or withdraw their submission. If a sample fails initial quality control the customer can resubmit replacement samples or withdraw their submission. If the customer chooses to resubmit their samples they must do so within a 6 week period. Sample submission after the 6 week period has elapsed will be considered as a new submission. If the customer withdraws their samples they must pay for any consumables ordered on their behalf.
What guarantees does the Ramaciotti Centre offer?
You are guaranteed to receive data that has met the QC metrics set out by the array manufacturer. Prior to sending data to the customer, the quality of the data output from each array is reviewed. Arrays that fail to meet the QC metrics set by the array manufacturer will be repeated free of charge. The only exception being if the customers has advised us to proceed with degraded or suboptimal sample in which case the customer is liable to cover all costs. The facility can only guarantee high quality results if all procedures are carried out with high quality nucleic acid. Poor quality sample will yield sub-optimal results. In this case the facility can not guarantee outcomes and the customer must accept responsibility.
How long will it take to get my data?
If we have the arrays in stock it will take approximately 3-4 weeks from receipt of your samples. Turnaround times for hybridization, wash and scan only are approximately 3 working days. Turnaround times on large projects and specialised arrays are dependent on array shipment times and project size. If you are considering a project with us which uses an uncommon array type please contact us we can often order in advance of receiving your samples.
What output files do I receive?
Affymetrix microarrays: You will receive a cell intensity file (CEL) file for each sample submitted. This file contains a single intensity value for each probe cell delineated by the grid. The CEL file is the file that is accepted by array analysis programs. You will also receive a quality control PDF for all the arrays in your project. Agilent microarrays: You will receive the extracted data as a TXT file and a quality control PDF for each array. For Agilent miRNA arrays you will also receive the processed GeneView file.
How do I access my data?
We will email you a link advising you that your data is ready to download, this link remains active for 14 days. Please ensure that you download your data promptly and securely back it up. Please note that the Centre’s terms and conditions state that it only stores customer data for a period of three months.
How do I analyse my data?
Microarray data can be analysed using a number of software packages. Commercial packages include Partek and GeneSpring. There are also free software packages such as R Bioconductor and Affymetrix Transcriptome Analysis Console. If you need help with data analysis please visit our bioinformatics page for information on services available to you.