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Sequencing | Sample Submission Guide

To submit samples please follow these five steps:

1. Online sample submission:

Before sending your samples please electronically submit them to the Centre using our Customer Sample Submission Portal.

IMPORTANT:
–  New customers are required to sign up for a user ID.  Applications will be reviewed and approved by the Centre before being activated. For further instructions please refer to our creating a User ID guide..
 – Follow the submission instructions carefully or the Excel spreadsheet will fail to upload.  Please refer to the guide to submitting samples for detailed instructions. 
–  The system will issue a unique ID for each sample it is important that you label tubes and plates with this ID. Samples that are not labelled with the unique LIMS ID will not be processed.
– If you are submitting for XTen sequencing please use either the barcodes or barcoded tubes provided to you and not the LIMS ID.

2. Application Specific Submission Criteria:

Please ensure that samples meet the application specific sample submission criteria. These can be found by clicking on the links below. If your samples do not meet these please contact us to determine if alternative methods are available.

Quick Links to Application Specific Sample Submission Criteria

Genomic DNA sequencing
RNA-seq
ChIP-Seq, MeDIP-Seq and Nucleosomal Sequencing
Amplicon/Microbial Profiling
Libraries (user supplied)
Long read: RNA & DNA (PacBio)
Linked read (10X Genomics)

IMPORTANT:
If we receive samples that do not comply with sample submission guidelines they will not be processed. You can either:
i) Resubmit samples. If samples are provided in plates the entire plate must be resubmitted. We will not cherry pick samples.
ii) Arrange for samples to be returned. The client must arrange courier collection and liaise with the Centre on the scheduling of this collection. The Centre is not responsible for any courier fees incurred for sample return.
Resubmitted samples must be labelled with a new unique LIMS ID. Samples will not be accepted or processed if they are labelled with a previous submissions project ID.

Samples that fail QC and do not proceed to sequencing will be attract a $15-$115 QC charge to cover costs (the amount charged is dependent on the service type).  For further information on the quality control procedures we use, please visit our Sample Quality Control page. If you wish to know more about preparation of RNA please download our RNA purification guide.

 

3. General Sample Submission Criteria:

Please ensure that your samples meet the following general criteria:

  • Samples must be intact and not degraded, as assessed by agarose gel, Bioanalyzer, TapeStation or LabChip GX.
  • Samples must be clean, 260:280 and 260:230 ratios >1.8. Lower 260:230 ratios are acceptable if a column purification method was used.
  • RNA samples must be free of genomic DNA contamination.
  • DNA samples must be free of RNA contamination.
  • Samples must be resuspended in nuclease free water and not TE.
  • Samples must be at the concentration and volume specified in the application specific sample criteria section above. 

When preparing your samples for shipping:

  • Ensure that your samples are randomised and in the correct order for processing in batches prior to shipping. The Centre will not randomise or reorder samples.
  • Projects with sample numbers <24 can be submitted in 1.5 ml microfuge tubes (non-screw cap, no parafilm or tape). Do not use strip tubes. Please consult with the Centre if you have a larger project (n>24) as submission is preferred in 96-well PCR plates. Large submissions in tubes may attract a handling fee.
  • Tubes and plates must be clearly labeled with the corresponding LIMS ID for each sample, refer to point 1 above.
  • Ensure plates are well sealed. Freezing plates before packing and shipping prevents loss of material and ensures that plate seals remains adherent at low temperatures.
  • The Centre can supply plates and seals on request.
  • The Centre accepts no responsibility for poorly sealed plates.

4. Payment:

– Please email a copy of your purchase order to the Centre. Please ensure that you provide your purchasing officer with the Centre’s email address.
–  Purchase orders are generated by your institution and are needed to authorise the transaction.
– If you intend to pay by credit card please email the Centre the following details: billing name, address, email and phone number.
– If you are internal to UNSW email us your project codes (Dept ID, Project ID, Fund Code).

IMPORTANT:
 – Failure to provide this information will lead to a delay in processing your samples.

 

5. Ship your samples:

On completion of the above samples can be shipped to the Centre.

Courier Delivery Address
Ramaciotti Centre for Genomics
Faculty of Science
Upper Campus Store, Room LG018
E26, Bioscience South
LG018 Loading Dock,
Via Gate 11 Botany Street,
UNSW Sydney NSW 2052
Australia
Tel: (02) 9385 1241
Hours: Monday to Friday, 8.00am – 4.00pm

In Person Drop off
The Ramaciotti Centre
Level 2, Biosciences South Building (E26)
Botany Street
UNSW Sydney, NSW  2052
Tel: (02) 9385 1658
Hours: Monday to Friday, 8.30am – 5.00pm
Please check that there will be someone available to accept them by calling (02) 9385 1658.

 

Application Specific Sample Submission Criteria

Genomic DNA Sequencing

  • Consult the table below for the amount, concentration and volume of DNA required for each assay. Please also ensure that samples also meet the general submission criteria, see point 2 above. If you cannot provide the amount stated below please contact us.
  • DNA must be double-stranded and not degraded as assessed by 0.8% agarose gel. Please include gel images when shipping your samples.
  • DNA concentration must be measured using the Qubit or Picogreen assay. Quantification by NanoDrop is inaccurate and should not be used for quantification. If this is not possible in your laboratory please contact us. 

Flip device horizontal to see full table

SERVICEAMOUNT REQUIREDCONCENTRATIONMINIMUM VOLUME
DNA Seq (PCR-Free)3 ug (350bp insert)
5 ug (550bp insert)
50 ng/ul
60 ng/ul
60 ul
80 ul
DNA Seq Nano (PCR)300 ng (350bp insert)
500 ng (550bp insert)
10 ng/ul
15 ng/ul
30 ul
30 ul
Nextera DNA400 ng20 ng/ul20 ul
Nextera XT DNA100 ng5 ng/ul20 ul

 

RNA-seq

  • Consult the table below for the amount, concentration and volume of RNA required for each assay. Please also ensure that samples also meet the general submission criteria, see point 2 above. If you cannot provide the amount stated below please contact us.
  • For submission of rRNA depleted RNA please verify rRNA depletion by Bioanalyzer and provide traces pre and post  depletion with your submission.
  • For rRNA depletion Illumina recommends Epicenter’s RiboZero kit or Ambion’s MICROBExpress kit.

Flip device horizontal to see full table

APPLICATIONINPUT & AMOUNT REQUIREDCONCENTRATIONMINIMUM VOLUME
mRNA Seq 3 ug total RNA70 ng/ul40 ul
Total RNA Seq - rRNA depleted submission300 ng rRNA depleted RNA10 ng/ul25 ul
Total RNA Seq RNA - human, mouse, rat 3 ug total RNA*100 ng/ul30 ul
Total RNA Seq RNA - bacteria or epidemiology3 ug total RNA*100 ng/ul30 ul
small RNA3 ug total RNA200 ng/ul15 ul

*If submitting samples for a low input assay please contact the Centre.

ChIP-Seq, MeDIP-Seq and Nucleosomal Sequencing

  • 10ng of the enriched immunoprecipitated material in a total volume of 20ul.
  • The quantity and quality of the input material should be checked by a fluorescence assay (Qubit or Picogreen) and by the quantitative real time PCR, respectively.
  • Please supply us with the fragment size range of the enriched material (200-600bp).
  • Where possible the size range of the immunoprecipitated material should be assessed by Bioanalyzer using the High Sensitivity kit.
  • IMPORTANT – It is not recommended to use salmon sperm DNA as blocking agent during the immunoprecipitation as it could contribute to contamination of your sequencing data.

Amplicon/Microbial Community Profiling

  • 15-20ul of DNA at a concentration of 5-10ng/ul (based on Qubit/PicoGreen quantification). 
  • DNA of high purity (260/280, 260/230 >~1.8).  
  • Samples should be submitted in 96-well PCR plates in consecutive columns with no gaps between samples.
  •  94 samples is the maximum number that can be submitted per plate. Two wells are required for positive and negative controls.
  • Samples must be amplifiable by PCR. Please check this prior to submission and provide a gel photo. 
  • If your samples require any special conditions or additives (i.e. BSA, DMSO) to amplify, please let us know at the time of submission.

Libraries (User Supplied)

  • >25ul of library at a concentration of 4nM (based on qPCR and/or Qubit/PicoGreen quantification, and Labchip/Tapestation/Bioanalyzer for sizing).
  • Library fragments up to 900nt.
  • If custom primers are required these must be supplied at the time of sample submission.
  •  Only one pool per run can be submitted, unless prior arrangements have been made.

Long & Linked Read

Please download our long and linked read submission guide for further information on DNA/RNA quality and concentration. 

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