How much sample do I need and how do I submit my samples?
Please refer to your quote for information on how much sample we require for analysis. Detailed instructions on how to submit samples can be found on our How to Submit Samples pages.
What happens after I submit my samples?
When we receive your samples we will send you an email you to let you know that they have arrived and if they have passed initial inspection. We will then contact you to let you know the outcome of sample QC (if applicable), this should be within a few days of sample submission. If all samples pass QC they proceed to library prep/assay, sequencing/array as requested. Turnaround times apply from the date of this email. The next time you hear from us will be when your data is ready to download.
How long will it take to get my data?
Turnaround times are dependent on project size and whether we have the required reagents in stock. We advise of the current turnaround times on our quotes. Be assured that we try our best to get data to you as fast we can, we don’t like to keep anyone waiting. If we anticipate a delay in project completion we will email you as soon as we are aware of it and advise you of the revised completion date.
How will my data be delivered?
Data is shared through a download link that is emailed to the sample submitter or via Illumina’s BaseSpace Sequence Hub.
What does the Ramaciotti Centre do to ensure quality?
The Ramaciotti Centre for Genomics is committed to providing competitive, high quality genomics services. We do this through:
- Consistently providing quality analytical services to our clients through data that meets or exceeds manufacturer’s specifications.
- Ensuring that all personnel are competent and qualified for the tasks they perform.
- Applying a quality management system according to the ISO/IEC17025 Standard.
All samples submitted to the Ramaciotti Centre must first pass initial quality control (QC) checks. A threshold for these checks has been put in place to ensure you receive data of the highest quality. We know from experience that samples below these thresholds may not perform well so advise clients to where possible meet or exceed them. Clients are notified if their samples do not pass QC and are advised of the next steps and possible solutions.
What is the best method to use for extracting RNA?
We do not recommend a particular method. If you have an established method that yields good quality, clean RNA please continue to use this. Please note that extraction methods that use organic solvents such as TRIzol Reagent may result in inaccurate quantification, due to the carry over of organic solvents. These solvents may compress the 260/230 ratio and often result in an overestimation of the amount of total RNA. A final column clean up method is recommended before submission.
What is the best method to use for extracting small RNA?
For small RNA arrays and sequencing 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. If you are using a commercial kit ensure that it retains small RNAs and follow the total RNA isolation protocol. Do not use the size fractionation or small RNA enrichment protocol. Please ensure that you use the same extraction protocol for all of the samples being analysed as different total RNA extraction methods may result in different miRNA profiles.
What is the best method to use for extracting genomic DNA for long read sequencing?
Our Long & Linked Read Sample Submission Guide provides general information on extraction, handling and shipping of DNA for long read sequencing.
Should I include replicates in my RNA sequencing or gene expression microarray experiment?
RNAseq or gene expression experiments should be treated like any other experiment in which you would as a matter of course include biological replicates. Consulting with bioinformatician on the number of replicates required for your experimental design is advisable as insufficient biological replicates will lead to an increase in the false discovery rate. There are a number of technical publications on RNA sequencing that may be of help. Schurch et al RNA (2016) on the number of replicates need for RNA sequencing and Corley et al BMC Genomics (2017) on the use of stranded protocols and single read versus paired end methods.
Where can I find general information on next generation sequencing?
Read Illumina’s sequencing introduction to find out more about short read sequencing or visit the Oxford Nanopore to learn more about long read sequencing. The Centre also runs a series of NGS focused workshops and seminars throughout the year. To learn more about these email us to sign up to our mailing list. There is a link at the bottom of our homepage.
Which sequencer or library preparation method should I use for my project?
We are here to help you plan your sequencing project and select the most appropriate sequencer and method, so please contact us for advice. The list of the sequencers that we have can be found on our technology page. A couple of handy pages are:
Illumina’s sequencing coverage calculator - to calculate the number of runs required to arrive at the correct coverage for your experiment.
Illumina Library Prep Selector tool - provides a guide on library prep selection.