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Submission guidelines

When submitting samples, please follow these simple guidelines:

Always make sure you have got the best possible quality of your RNA or DNA - to get good libraries, you need good starting material!

If you quantify your nucleic acid, use a fluorescent dye (Qubit, picogreen), and avoid the nanodrop! We will do a QC wherever possible, so don’t worry if you have not got access to this.

 

RNA samples

RNA can be extracted using any commercially available RNA extraction kit.

It is necessary to include a DNAse treatment to eliminate any DNA background signal in your data.

If you are performing bioanalyzer QC yourself, aim for RIN values for >8. We routinely do this quality check for you, so you do not have to have access to a bioanalyzer/ tapestation.

Your samples should be submitted in RNAse free water, and on dry ice if at all possible. Please make the labelling easy and understandable! We like numbers!

We have a variety of different RNA protocols, which are mainly aimed at different input amounts. In general, we would like to have as much RNA as you can isolate in the lowest possible volume. The type of protocol we chose for your samples will depend on the outcome of your sample’s QC. However, we are constrained by the input amounts of the different protocols:

Low input samples from 250pg to 10ng will be processed with Takara’s SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian. The required input volume for this is 8ul, the sample you supply will need to be in no more than 13ul volume.

Low input samples from 10ng to 100ng will be processed with the Nugen Ovation RNA-Seq Systems 1–16 for Model Organisms. The required input volume for this is 5ul, the sample you supply will need to be in no more than 10ul volume.

Samples with higher input (100ng to 1000ng) can be either depleted of ribosomal RNA or selected for PolyA.  (PolyA is often chosen when transcript counting and cost limitation are what is required. Ribosomal depletion allows for non-coding RNA to be present and has less 3’ bias, but is more costly.) For these two methods we require the samples to be in volumes of 10ul (rRNA depletion) or up to 40ul (PolyA).

 

DNA samples

Genomic DNA should be free of RNA, and you should check the integrity and size on a 1% gel before submitting.

Clean ChIP DNA should be submitted after you have done the chromatin immunoprecipitation in a volume not larger than 15ul. Do not attempt to measure ChIP DNA in a nanodrop, it will not be accurate enough. Please check the fragment size of your input DNA, and please let us know if your fragments are longer than 500bp.

Your samples should be in water and submitted on ice. If samples have been exposed to phenol or other organic solvents, they should be run through a cleanup column prior to submission to avoid contaminants that may inhibit the activities of enzymes used in subsequent steps. Please make the labelling easy and understandable! We like numbers!

 

Submission of samples into the system

We require each project to be submitted into the online submission system:

https://genomics-sci.atlassian.net/servicedesk/customer/portal/1

Please create your own account for this system, none of your university affiliations are registered.

We will require information about you, your group, some GM and biosafety assessment numbers, your grant code, and of course the project. Please see our submission help file for specific questions about these points!