Please Note: NZ Genomics will no longer be accepting new projects from 1 July 2017. Visit our Services page for further details.

FREQUENTLY ASKED QUESTIONS:

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NZGL PROCESSES AND PRICING

How much does it cost?
The cost varies, depending on the services required, the scope
of the project and your funding source.
Currently, the discount provided to publicly-funded projects is around 35 to 60% off the total commercial cost. We are happy to look at your project and, once our team has scoped the project, provide a no-obligation quote. Just fill out and submit the project enquiry form.
What kind of projects can you help me with?
NZGL's collaborative structure means it has an impressive depth of skills across its people and the flexibility to handle both large and small projects. The Services page outlines the full list of next-generation sequencing, microarray, bioinformatics support and Bio-IT services available. You can contract a full, end-to-end service, or specific the particular elements you need completed.
How does the process flow?
The process is described on the Services page.
How do I initiate the process?
Use the project enquiry form to get the ball rolling. This provides NZGL with enough information to begin developing a project scope and, ultimately, a quote.
What timeframes should I allow?
It will depend on the service you require, the complexity of your project and its size. Until a contract is in the pipeline and we know the immediate capacity of the specific services, it is difficult to answer this definitively. However, just ask and we will come back to you with a timeframe estimate at the same time as your quote.
When can I submit my samples?
Do not submit your sample until it is requested. When your NZGL Services Agreement has been finalised, you will be provided with sample submission and quality control information. NZGL cannot take any responsibility for unsolicited samples.
Can I get help with writing grant applications?
We strongly encourage you to contact NZGL for assistance with your grant application. You can do this at one of our bioinformatics Q&A sessions or via the NZGL online enquiry form.
Can I get help with experimental design and platform choice?
All New Zealand researchers can receive up to two hours of free (and obligation-free) scoping and design advice. If required, more in-depth advice can be provided as part of an NZGL project.
I’m not located in New Zealand. Can I use your services?
Yes, of course! NZGL services are available for any customers. NZGL’s cost model provides a discounted price for researchers with NZ government-based funding, but services are still available to users outside NZ on a full cost recovery basis.
How does your subsidy/discount model work for New Zealand-based customers?
NZGL’s goal is to provide a nationally coordinated genomics research infrastructure accessible to all New Zealand researchers and institutions. To accomplish this, NZGL receives funding from the New Zealand Ministry for Business, Innovation, and Employment (MBIE). This funding is directed towards enabling New Zealand research, so is used to subsidise the cost of NZGL’s genomics and bioinformatics projects for NZ-based researchers. The full cost of performing a genomics research project includes staff salaries, equipment depreciation, and operating expenses. NZ-based researchers (regardless of affiliation or institution) are charged only a portion of these full costs, with the remainder paid by NZGL through its MBIE funding.

BIOINFORMATICS SUPPORT

How does the bioinformatics support work?
The best place to start is by filling in a project enquiry form. This gives us some baseline information to understand your requirements. From there, we can contact you directly, if we need more information, then provide a quote. We match your project to an appropriate bioinformatician and that person becomes your point of contact for the duration of the project. The bioinformatics support service is very flexible, so don't be shy to ask about any projects - no matter how small or potentially challenging.

A reminder that NZGL provides up to two hours of free bioinformatician advice, which you can use to scope out your project and establish any pitfalls or opportunities, before you start properly. And there are also the regular “Talk to a bioinformatician” sessions on the Auckland, Massey and Otago university campuses.
How do I get in touch with someone about bioinformatics support services?
The project enquiry form is a great place to start, as it provides us with the basic information on your project. We can then give you a call to discuss any specific queries you have and/or fill any knowledge gaps.
What is the process around contracting bioinformatics support services?
First, fill in the project enquiry form. NZGL will arrange for the appropriate bioinformatician to contact you if any additional information is required. Following this, you will receive a quote for services and, if you wish to proceed, we will sign a contract and work begins.
How long will my project take?
You will be given an indication of timeframes, at the point when you receive your quote. Timeframes vary, depending on the nature and the size of the project.
I have a grant application coming up. Can I get a quote for the bioinformatics support work I will need to contract?
Yes. However, bioinformatics projects can be complex and therefore take some time to scope. Please contact NZGL early in the grant application process to avoid disappointment.
Can I ask NZGL to analyse data from other providers?
NZGL is happy to analyse data generated by other providers.
Can I ask NZGL to upskill or coach me to analyse data myself?
Yes. We run a series of workshops and seminars that may suit your needs. One-on-one coaching and training can also be provided as part of an NZGL project, with associated bioinformatics time included in the contract.

BIO-IT

What is Bio-IT?
Bio-IT refers to the purpose-built computation infrastructure that stores and processes genomics data and the software applications available to analyse that data. This service is professionally managed and dedicated to genomics data storage and analysis.
How can I access the NZGL Bio-IT resource?
When you contract Bio-IT services through NZGL, you will be provided with an account and password that provides access to the resource and your sequence data (if it was generated within NZGL). You are also given access to specialist IT staff who can assist you in becoming “operational”. Access to the system is monitored through a comprehensive security system.
Can I use Bio-IT for data that has been sequenced by myself or at another facility?
Yes. NZGL runs a Globus Connect Endpoint that supports the robust transfer of large files in and out of the system. By special arrangement, we can also provide a facility to load data from portable hard drives.
What is the pricing structure for Bio-IT?
The cost varies depending on the scope of the project and your funding source (which determines if you are eligible for a discount). We are happy to look at your project and provide a no-obligation quote. Just fill out and submit the project enquiry form. Many projects receive a substantial discount and we also support general long-term access arrangements, which are very cost effective.
I have a project involving a number of collaborators. Does the NZGL platform support this type of project?
Yes. The Bio-IT platform was designed from the ground up to support collaborative working. We support the ability for multiple parties to access common data sets and we provide access to collaboration tools – to assist communication between partners. We can also provide access to NZGL bioinformaticians, who may be working with you on data analysis. The system has a robust security and access model to support this collaborative access.

NEXT-GENERATION SEQUENCING SERVICES

Does NZGL have specific sample requirements for RNA and DNA?
The amount and minimum quality requirements for samples are project dependent. Please refer to our pages on sequencing and microarray services for specific details.
Does NZGL offer a DNA/RNA extraction service?
NZGL does not provide a sample preparation service, but we may be able to offer advice about your preparation strategy. NZGL does not have preferred suppliers of DNA/RNA extraction reagents. Please refer to NZGL guidelines for sample submission to ensure your methodology meets our minimum standards for quality.
What equipment do I need in my lab to prepare samples for submission?
NZGL genomics facilities require information about the purity, integrity, and quantity of your DNA/RNA samples. These metrics require methods such as:
• Purity: UV spectroscopy including OD260:280 and OD260:230 ratios e.g. Nanodrop
• Integrity: Agilent Bioanalyzer or high-percentage agarose gel
• Quantity: Concentration using fluorometric methods, e.g. Qubit (Nanodrop is not suitable)
Further information about specific requirements can be found on our services page.
What happens if my samples don’t meet your requirements?
You will be asked to submit pre-submission sample QC information to the nominated genomics facility prior to sending your actual samples. If this information is not complete or fails to meet facility minimum standards for quality and quantity you will be contacted by the facility to discuss available options. Options may include refining the sample extraction method, postponement or project cancellation. If a project is cancelled you will be liable to pay for any costs incurred by NZGL as per the Terms and Conditions of your NZGL Services Agreement.
Can I continue my project if my samples do not meet requirements?
You will be given an opportunity to continue using a “best efforts” approach. Our genomics facility will select the most appropriate library method for your samples and prepare the sequencing libraries. They will then provide a sequencing recommendation and you will be asked if the project can be continued at your risk. If a project is cancelled you will be liable to pay for any costs incurred by NZGL as per the Terms and Conditions of your NZGL Services Agreement.
What happens if I can't meet the contractual sample submission deadline?
All NZGL genomics contracts include a final date for sample submission. If you cannot provide all samples to the designated service facility before this date, please contact the NZGL office as early as possible, quoting your NZGL project ID, to provide a new estimated delivery date. The NZGL office will discuss options available including a contract variation to extend the delivery date, postponement or cancellation. Please refer to the NZGL Services Agreement Terms and Conditions for information regarding project cancellation.
How long will you store my samples for?
All remaining sample(s) following library preparation are securely stored by the genomics facility for at least three months. You will be notified a minimum of 10 days prior to sample disposal. Samples can be returned for a small handling fee, however, we do not recommend that you submit your entire sample to the facility.
Can NZGL prepared libraries be re-sequenced as part of a new contract?
All sequencing libraries are securely stored by the genomics facility for at least three months. You will be notified a minimum of 10 days before library disposal. Please enquire with NZGL to find out if the re-sequencing of a prepared library is possible. Please note, prior to re-sequencing, the libraries will be subjected to facility QC checks to ensure they are still suitable for sequencing.
What library QC checks do the facilities use to determine suitability for sequencing?
Sequencing libraries are accurately quantified using a fluorometer (e.g. Qubit) or qPCR and run on an Agilent Bioanalyzer High-Sensitivity labchip or DNA 1000 labchip to assess the size distribution and presence of any contaminants (such as primer-dimer, or other extraneous peaks). All libraries prepared for HiSeq 2500 sequencing undergo a MiSeq QC run. This data is not made available to the client.
What library types do NZGL offer for Illumina sequencing?
The “Illumina sequencing applications” table provides details on library types and associated sample requirements. NZGL also offers custom library preparation if suitable for your project design.
Can I prepare my own library and submit for sequencing?
NZGL can accept client-prepared sequencing libraries. Please contact NZGL for terms and conditions associated with this library type.
What sequencing platforms are available?
NZGL facilities have various instruments, including Illumina HiSeq2500 and MiSeq plaforms and an Ion Torrent Personal Genome Machine. See the services page for more details.
How do I choose the best sequencing platform for my needs?
NZGL genomics scientists and bioinformaticians are experts in helping you to identify the best approach for your project, including the choice of sequencing platform. Please use the project enquiry form to help us understand what you want to achieve.
What format will my MiSeq data be delivered in?
The data generated from the Illumina MiSeq platform is provided in FASTQ format.
What data will I expect to receive from the HiSeq2500?
All sequence data will be provided as compressed FASTQ files with an associated FASTQ report. For more information, visit the Otago Genomics and Bioinformatics Facility website.

MICROARRAY

What microarray platforms are available?
NZGL facilities have Affymetrix GeneChip platforms and can run any Affymetrix cartridge-format array. For more detail, see the Microarray page.
What types of microarrays can you run for me?
Our facilities can run any Affymetrix cartridge array. At this time, we are not able to run other Affymetrix array formats (such as Axiom plate-based arrays) or arrays from other manufacturers.

NANOSTRING

What samples can be used for nanoString analysis?
Almost any samples (including cell lysates single cell preps and other biological fluids) may be suitable for analysis. Contact the Otago Genomics and Bioinformatics Facility for information on how to proceed with non standard sample types.
What is the minimum number of samples and targets (genes) processed in nanoString technology?
The consumables for all applications are provided for a single use in sets of 12. We therefore recommend 12 as the minimum number of samples. The Custom CodeSets have minimum setup fee, which equals to 28 targets in Gene expression application and 50 targets in CNV and ChIP String applications. The nCounter Elements TagSets are also provided in multiples of 12 samples and 12 targets.
For more information, visit the Otago Genomics and Bioinformatics Facility website.
How long will my nanoString project take to complete?
Project duration is dependent on the complexity of the CodeSet design, synthesis and delivery of consumables and receipt of samples to the facility.
For more information, visit the Otago Genomics and Bioinformatics Facility website.
What is the output of nCounter?
It is a comma-separated (.csv) file with the columns containing numbers for molecule counts detected in your samples and rows containing probe names. The files can be opened as an Excel spreadsheet.
Where can I find additional information about the nCounter gene expression, CNV, single cell and miRNA pre-built panels?
See www.nanostring.com for more information. Gene lists and application notes can be downloaded and searched for your gene(s) of interest. Contact NZGL, if you cannot find the required information.
For some indicative pricing information, visit the Otago Genomics and Bioinformatics Facility website.
Can I add my favorite genes to a pre-built nCounter panel or Custom CodeSet?
The nCounter PanelPlus or CodeSet Plus options enable additional genes to be added to pre-built panels, expanding their utility. Contact NZGL for prices and options. Be aware that Custom CodeSet design can take one to three weeks, depending on organism and project complexity. nanoString will provide a Custom CodeSet Design for your approval. This can be altered at any time up until you sign and return the CodeSet documentation agreeing to synthesis. Pre-built panels can be ordered directly from nanoString US upon receipt of a signed NZGL service agreement. Your NZGL service agreement will provide you with a completion date. If this is not satisfactory, contact NZGL to discuss your requirements.
Can NZGL assist with analysis of my nanoString data?
NZGL currently provides three tiers of data analysis service for all nanoString projects:
  1. Raw data only. QC assessed.
  2. Normalised raw data. Non-specific binding levels are estimated by the presence of 6 to 8 negative controls. The probe values are then adjusted by applying an estimated non-specific binding activity. A csv file will be provided with the corrected value).
  3. Full statistical analysis of data. This analysis will be tailored to the researcher’s needs and can include differential expression analysis, clustering or pathway analysis.

FIND WHAT YOU NEEDED?

If not, fill in our general enquiry form and a member of the NZGL team will answer your question.

A COLLABORATION OF:

WITH THE SUPPORT OF:

Ministry of Business, Innovation & Employment