What kind of samples can I can submit for sequencing?

RNA:

  • Total RNA
  • FFPE derived RNA
  • Total Nucleic Acid
  • DNase-I treated RNA

DNA:

  • Genomic DNA
  • FFPE derived DNA
  • Total Nucleic Acid
  • Chromatin Immunoprecipitated (ChIP’d) samples

Tissues for Nucleic Acid extraction:

  • FFPE blocks or sections
  • OCT sections
  • Fresh frozen sections
  • Cells

Constructed Libraries:

Sequencing of other starting material may also be available. Check out our staring material requirements for more information.

Please contact us with your specific project needs, to confirm our ability to process your samples.

What library construction strategies are provided?

The following library construction strategies are available:

  • FFPE-Genome
  • PCR-Free Genome
  • Low input DNA
  • Bisulphite
  • ChIP
  • miRNA
  • ssRNA, polyA+
  • mRNA using strand specific protocol
  • Ribodepleted strand specific RNA
  • TCR/BCR
  • Exome and custom capture

Please contact us if you have a strategy in mind but it is not listed here.

How should I isolate my RNA/DNA or immunoprecipitate my chromatin?

We can advise on extraction of RNA, isolation of DNA or immunoprecipitation, but cannot provide optimized protocols.

All isolation protocols will need to be optimized in your own lab. Some variability is unavoidable when working with biological samples.

Please See here for starting material requirements

What is the cost of library construction and sequencing?

The costs associated with library production vary depending on starting material. Please contact us for a quote or Statement of Work (SOW).

What happens if the run or a library fails?

The solution will depend on the source of the problem. Several quality checks are included in the process of constructing libraries and sequencing, in an effort to minimize the potential for failure.

  1. DNA samples are quantified upon receipt of samples in advance of library construction. RNA samples are quality and quantity checked in advance of library construction. You will be contacted if your sample falls below the required total mass or is degraded and not suitable for library preparation.
  2. If library construction fails, the collaborator will be consulted to find a solution. There is no standard policy, as failure can be attributed to many causes. If the cause is found to be sample related, a replacement sample may be submitted. 
  3. For samples requiring multiple lanes of sequencing, a single lane is initially run to assess library quality. If the lane fails any of several quality metrics, the Quality Control team reviews the data to identify the source of the problem. Concerns about library construction are reported to the customer to discuss possible solutions and options. Sequencing run quality metrics are reviewed by the lab to ensure high quality sequence is produced. Runs failed due to instrumentation/technical issues will be repeated at no cost to collaborator. The Quality Control team reviews the content of the sequence data to ensure several quality metrics are met. Failures are investigated to determine the root cause and are reported to the collaborator to discuss possible solutions and options

Please also check the QC Alerts document for any alerts you may see in your Illumina Data file

How many lanes should I run and how do I determine sequencing coverage?

Sequencing requirements will vary between researchers and between samples. The number of sequencing lanes required depends on the experimental design and your sample.

Important variables include:

  • sample quality
  • sample quantity
  • genome size
  • availability of a reference genome for comparison
  • goal(s) of the project

Illumina also has some helpful resources to help determine this. 

Are there any specifications for genomic samples or libraries submitted for sequencing on the HiSeq X?

HiSeq X sequencing is available for whole genome samples (human and other) to an average depth of coverage of 15X or greater.

Sequencing of bisulphite or phasing libraries to an average depth of coverage of 15X or greater, is also permitted but unsupported.

Illumina does not provide any assurances or guarantees that the performance of the HiSeq X instrument will match published specifications when used for unsupported applications.

Are there specifications for submitting Chromatin Immunoprecipitation?

If our collaborators choose to submit cells, we require them to be snap frozen pellets. A total of 1M (per sample) is the recommended amount if all 6 marks are done for one sample. The 1M cells (per sample) can be submitted in one tube

Are there any specifications for samples or libraries submitted for sequencing on the NextSeq 500?

The NextSeq 500 has a minor restriction on index sequences that can be used when barcoding libraries. To detect a cluster during template generation, there must be at least 1 base other than G in the first 5 cycles.

Do I have to cite the GSC for the sequencing work performed when I publish my research? How should I cite work performed by the GSC?

We require our collaborators to acknowledge the work performed by the GSC in the following ways depending on the level of collaborative effort between the GSC and the researcher:

If the data was generated as a fee for service (cost-recovery collaborative service alone, i.e. when no intellectual contribution has been made). The GSC should be cited using either of the methods below:

  • In peer-reviewed publications incorporate the following sentence into the Acknowledgements section of the article: “The authors wish to acknowledge the BC Cancer Genome Sciences Centre, Vancouver, Canada for [activity]”.
  • Or alternatively, the GSC can be cited in the Materials and Methods section. A suggested sentence for inclusion is: “[Activity] was performed by the BC Cancer Genome Sciences Centre, Vancouver, Canada”.

Where intellectual contributions have been made by researchers at the GSC, collaborators are required to discuss potential and pending publications based on these contributions with the relevant GSC scientists or staff to identify appropriate coauthorship. This will ensure that our scientists and staff receive the appropriate credit for their work, and enable them to advance their careers.

The BC Cancer Genome Sciences Centre (GSC) tracks contributions to the wider scientific community. This is a means to measure our ongoing support for the activities of our collaborators, as well as to ensure we meet the requirements of both our funding partners and our charter as a non-profit agency.

What are the Histone modification core marks provided by the GSC?

At the GSC the histone modification core marks are the following:

  • H3K4me1
  • H3K4me3
  • H3K9me3
  • H3K27me3
  • H3K36me3
  • H3K27ac
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