How to fill the submission form

Sample submission form:

https://www.sequencing.uio.no/forms/sample-submission-form-(illumina).docx

Sample submission table:

https://www.sequencing.uio.no/forms/sample_table_96_template.xlsx

Section 1: General Sample Information

Enter text/check boxes as required. Provide buffer information for the buffer your samples are delivered to us in, not the buffer they may originally have been extracted in. Note that different DNA amounts are required if you are submitting DNA for the NSC to prepare libraries (often called “sample prep”) on your behalf, or if you have prepared libraries yourself.

If your submission consists of more than one sample type (e.g. both DNA for PCR-free library and RNA for miRNA library construction), please complete two separate copies of the submission form.

Section 2: Sample prep requested

Please tick the appropriate box for your needs (mandatory if requesting that the NSC performs sample prep). This section should be left blank if you have prepared your own libraries.

Paired end library insert sizes. For DNA samples, average insert sizes can be delivered at either 350 bp or 550 bp (valid for TruSeq DNA preps, for Nextera DNA FLEX the insert size is ca. 450 bp). For low numbers of samples (<8), library insert sizes can be tailored in the range 100-700 bp, but only using DNA preps that employ PCR. For RNA samples, we employ fragmentation conditions that produce insert sizes with a range of approximately 130-310 bp (median approx. 190 bp).

Section 3. Sample Information table

Complete the table, paying attention to the information below. If you have >16 samples, please submit in 96-well plates and complete the Excel template table instead, available for downloaded here: http://www.sequencing.uio.no/forms/sample_table_96_template.xlsx

Sample Name

Names may ONLY consist of letters, numbers and the hyphen (-). NOT UNDERSCORE (_). Do not use any other characters, including æ, å, ø spaces or period. Character limit = 16. A simple numbering is recommended in addition to more complex name details (e.g. 1-abc, 2-abc). Please also write the submitters name on individual tubes / plates – we can receive hundreds of samples in a week.

Sample Type

Detail the type of sample you are submitting, NOT the prep type you wish performed / have performed.

* Please choose from the following abbreviations. Use your own if none are appropriate, but provide an explanation:

LIBRARY          = Ready-prepared libraries

gDNA              = genomic DNA

Tot. RNA         = total RNA

mRNA             = purified mRNA (poly-T enriched or rRNA-depleted)

cDNA               = cDNA

mi-RNA           = purified short RNAs (please specify length)

SeqCap            = captured/enriched DNA

ChIP                = chromatin immunoprecipitate

meDIP             = methyl DNA immunoprecipitate

BS DNA           = bisulfite converted DNA

amplic             = PCR amplicons      

§ If combining multiple samples per lane, please indicate which samples may be combined together. If you have already performed sample library prep and Illumina-compatible indexing, also detail which index codes (manufacturer, index position in adapter, and index sequence) were used for each sample.

† If you have used any whole-genome amplification techniques that attach nucleic acid adapters/linkers to your DNA, provide details here (including sequence). In addition, if you have used restriction enzyme digestion of your sample, this should be noted here. Both of the above will result in many sequences starting with the same bases, which requires special handling during Illumina sequencing.

Section 4. Sequencing Information Required

If you are unsure/did not receive a recommendation from us as to which kind of sequencing is appropriate, please get in touch with us using the email address below, or complete the project request form available at http://www.sequencing.uio.no/forms/

The type and length of sequencing have a major effect on the cost of your project, and sequencing of your project cannot begin without this information. Information about the available at NSC Illumina sequencing options can be found here: Illumina sequencers

Please also give a brief description of your project goals, which will help us ensure you get the most appropriate sequencing type and length. Norwegian projects involving human subjects are required to provide a REK number.

Section 5. Data Delivery:

Please select your preferred data delivery method. For non-sensitive data, it is usually convenient to select a download option. Sensitive data can only be delivered on hard drives or through secure networks. If you have a secure network available to which we may upload the data, please contact us to arrange access.

Notes on sequence and quality score output files
Output files can be up to 1 Tb in size, depending on the run type and length. Sequence is output as a file containing the sequences of all clusters in the sample and the associated quality scores in fastq format (see http://en.wikipedia.org/wiki/FASTQ_format). In the case of paired-end reads, the base calling software outputs two files for each sample (one for each end). These files are sorted, so that the nth read in the first file originates from the same cluster as the n-th read in the second file.

Data storage policy:  Image files are not stored, and other associated run data will be deleted soon after the data is delivered. Fastq files along with reports will be stored for a period of 2 months from the date of the delivery mail, after which they will be deleted.

Section 6. Contact, Billing & Delivery details (All fields mandatory):

We require a single person to act as our contact regarding sample preparation. This person must also be capable of providing information on billing & data delivery, but you are required also to enter the name of the relevant purchasing official to whom the bill should be addressed. SUBMISSIONS WITHOUT A VALID PURCHASE ORDER NUMBER WILL BE REJECTED. Should you require an estimate in order to generate this number, please get in touch with us at the address below. If your institution does not use an order number system, then please enter “not applicable”.

Note that additional information is mandatory for internal OUS orders.

Registering us as a service provider: The NSC is not a legal entity, and you will therefore not find us in the Brønnøysund Register. Your invoice will be sent from either Oslo University Hospital or the University of Oslo, depending on which node will sequence your samples (if this is unclear, please contact us on post@sequencing.uio.no to clarify). Banking details can be provided if necessary.

Pricing: Our prices vary in accordance with USD:NOK exchange rates at the time reagents are purchased for your project. Please contact us for an estimate for your project. We provide quotes, usually valid for 30 days, which you can use to raise a purchase order number for your submission.

Section 7. Sample Delivery Information

Please submit the completed submission form by email prior to making your delivery. During seasonal holiday periods, we may not accept submissions – please check www.sequencing.uio.no for news prior to sending samples. Provide carrier information, or if delivering in person, please check that we are available to receive you.

DO NOT send samples by registered post or TNT carrier (they may be delayed for several days in internal post before we are notified that our signature is required to collect the package).

A map can be found here:

http://www.sequencing.uio.no/contact/

Detailed directions can be provided by mail upon request.

About the NSC:

The NSC is a collaborative venture between Oslo University Hospital and the University of Oslo. General inquiries should be addressed to our common email address post@sequencing.uio.no.

If you have already received instructions on which node to use, the individual nodes can be reached as follows:

OUS Node                                                            UiO Node

Tel: +47 2211 9724 / 2301 6419                          Tel: +47 2284 4446                           

Email: ous-seq@sequencing.uio.no                 Email: cees-seq@sequencing.uio.no

 

 

Published Mar. 24, 2020 4:21 PM - Last modified Apr. 7, 2020 4:38 PM