Library Construction and Sequencing

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

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
• Exome and custom capture

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

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

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

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

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. 

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.

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

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.

In order to gauge our scientific impact we attempt to track our contribution to the wider scientific community. This is done as part of 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. In order to achieve this, we require our collaborators to acknowledge the work performed by the GSC in any or all of the following ways:

1. The GSC does not request or require co-authorship on publications when data has been generated through their cost-recovery collaborative service alone, i.e. when no intellectual contribution has been made.
2. Where intellectual contributions have been made by 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 co-authorship.
3. At a minimum, acknowledgement of the work of the GSC should be included in peer-reviewed publications. The following sentence can be incorporated into the Acknowledgements section of the article: “The authors wish to acknowledge Canada's Michael Smith Genome Sciences Centre, Vancouver, Canada for [activity]." A full list of funders of infrastructure and research supporting the services accessed can be found on the About Us page. 
4. In addition, acknowledgements should appear in the text of peer-reviewed publications, for example in the Materials and Methods sections. A suggested sentence for inclusion is: “[Activity] was performed by Canada's Michael Smith Genome Sciences Centre, Vancouver, Canada”.

We would be very pleased to receive notification when collaborators publish papers acknowledging the GSC.

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

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