Illumina Submission

HOW TO MAKE A SUBMISSION

Submission is simple – just fully complete the submission form and send it with required attachments, when fully complete, in a single mail to post@sequencing.uio.no, wait for our reply that your submission is accepted, then bring or ship your samples to the address advised by the NSC staff in their reply (either OUS or UiO, shipping addresses are at the back of the submission form).

If you need a price quote in order to obtain a purchase order number, contact us to obtain one on post@sequencing.uio.no – do not send an incomplete form and the purchase information later.

Required attachments (documenting sample size and integrity)

Unless agreed with us in advance, you are required to provide both:

1. Our submission form (and sample submission table, if submitting more than 16 samples or a pool) (http://www.sequencing.uio.no/forms/samplesubmissionforms.html)

2. Gel image or BioAnalyzer (or equivalent method) traces of your samples / libraries.

DNA:   For genomic DNA samples, an agarose gel showing high MW DNA with no degradation is most appropriate (indicate relevant marker sizes, and amount of sample loaded). For ChIP samples, input DNA must be shown.

RNA:   A BioAnalyzer trace/list of RIN numbers is preferred. Agilent Bioanalyzer RNA Integrity Number (RIN) should be > 7.  Gel images showing rRNA are also acceptable, in which case samples should have a 28S/18S ratio >1.6.

LIBRARIES: For prepared libraries, a bioanalyzer trace or equivalent is most appropriate.

Sequencing options

Information about the available at NSC Illumina sequencing options can be found here: Illumina sequencers

SAMPLE REQUIREMENTS

Sample amounts

Please find the individual for each library prep sample requirements in the respective tab in the menu on the right.

As a general rule, more DNA/RNA is better, so please provide more than the recommended sample amounts listed below if you can. Using the minimum amount increases the chances of failed preps. We may also be willing to attempt library preparation with amounts lower than the given minima, but this must be agreed with us in advance of submission, and you must nonetheless pay the cost of consumed reagents in the event of prep failure.

Samples with high genomic DNA concentrations (>1 µg/µl) cause problems with our automation due to their viscosity, so are not acceptable. Please dilute your samples to under this limit and re-check their concentration. Do not send DNA or RNA samples, even at high concentrations, in less than 5 µl, as this makes use of automation or multichannel pipettes difficult.

Sample integrity

RNA: Agilent Bioanalyzer RNA Integrity Number (RIN) should be > 7

Genomic DNA: for Nextera DNA flex prep, the sample should have high MW with no degradation. For other preps, fragmented DNA (as from FFPE samples) is acceptable, as the DNA will anyway have to undergo fragmentation by sonication prior to

Sample purity

For DNA and RNA samples the 260/280 ratio should fall in the range 1.8-2.1 and the 260/230 ratio within 1.8-2.4. Different requirements apply for ChIP samples - please see the application-specific tab.

Note that purity measurements (spectrophotometer absorbance) must be documented for each sample in either section 3 of the Submission form (if less than 16 samples) or in The Sample submission table (in Excel format, that you can download from the Forms section on this webpage) (if more than 16 samples).

Sample concentrations

We do not insist that you equalise the concentration of all samples in your submission. However, your samples will be processed faster if you do so, and we encourage this practice. Please see the application-specific tab for required sample amounts and accepted buffers.

Accepted buffers

See the application-specific tab for exact information. Generally, except where specified, do not use buffers containing EDTA, as this will inhibit the enzymatic steps of sample library preparation. If you must concentrate your samples to achieve the recommended minima below, please bear in mind that the final concentration of buffers will affect downstream performance. Do not submit samples in >10mM Tris or other concentrated buffer. We do not accept lyophilized or precipitated samples. Samples delivered in inappropriate buffers will either be returned to the user or subject to additional cleanup costs of 1000 NOK/sample at our discretion.

Accepted tubes/plates and labeling

Each tube/plate must be marked with the user’s name and date, in addition to sample name. When submitting >16 samples, use 96-well PCR plates, not 8-well stripes or 0.5 ml tubes, (filling in columns – see figure below). Lower numbers of samples should be submitted in 1.5-ml Safelock Eppendorf tubes (please don`t tape Parafilm around the tubes). We do not accept precipitated/dried samples.

Correct layout for filling samples in 96-well PCR plates (i.e. filled by columns from left side, not  by rows). Do not leave empty wells or gaps!
 

Failure to follow these guidelines voids any guarantees on library preparation or run yields!

 

 

 

Published Mar. 20, 2020 10:50 AM - Last modified Mar. 31, 2020 9:58 AM