Services
As a national sequencing core facility, the NSC offers sequencing services on the GS FLX from Roche/454, and HiSeq 2000 & MiSeq instruments from Illumina and the PacBio RS from Pacific Biosciences. In addition, the NSC is in the process of installing the PGM from IonTorrent/Liife Technologies.
For an overview and comparison of the properties of the different machines, please refer to our HTS introduction.
For more in-depth information on the individual machines that we are currently making available to users:
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HiSeq | Available as a service |
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MiSeq | Available as a service |
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GS FLX (454) | Available as a service |
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PacBio | Available as a service |
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PGM (Ion Torrent) | Currently installing |
Run parameters (2 flow cells, each with 8 lanes available for user samples):
- Up to 3 billion reads (6 billion paired end)
- Single-read or paired-end
- Read lengths of 50 or 100 bp
- Total output up to 600 Gbp per run. Run durations up to 12 days.
Additional Run parameters (HiSeq 2500 only)
In addition to the parameters above, the 2500 instrument can also be run in a "rapid" mode that offers lower throughput but at greater speed. This also allows longer read length (all at increased cost per base compared to the regular runs).
- Up to 600 million reads (1.2 billion paired end)
- Read lengths up to 150 bp
- Total output up to 180 Gbp per run. Run duration approx. 40 h.
Applications include:
- Genomic DNA sequencing
- mRNA sequencing
- smallRNA/microRNA sequencing
- Epigenetics
- Chromatin immunoprecipitation sequencing
- DNA methylation
Most samples can be run as either Paired-End (PE) or Single-Read (SR) experiments
Workflow:
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Sample Submission:
A sample submission form for needs to be filled out when submitting a sample for Illumina sequencing. You must also download the separate guideline file (Guidelines for completion of Illumina sample submission form). The form should be filled out (light grey boxed sections 1-6), saved under a file name that includes name and date and submitted as soon as possible before delivery/submission of your sample(s). The completed form should be sent by email to: ous-seq@sequencing.uio.no.
Run parameters (single flow cell with 1 lane for samples):
- Up to 15 Million reads (30 Million paired end)
- Fast run times - 39 hours or less
- Read lengths of 50, 150 or 250 bp (300 bp reads expected in late 2013)
- Total output up to 8.5 Gbp per run
Applications include:
- Small genome DNA sequencing (de novo & resequencing)
- Metagenomics studies (including rDNA)
- Amplicon sequencing
- Targeted resequencing, such as gene panels
- Control of libraries for large projects
- smallRNA/microRNA sequencing
- Epigenetic studies with few samples
Workflow:
The workflow for the MiSeq is very similar to that of the HiSeq 2000 instrument. However, we aim to provide a much faster turnaround time for MiSeq projects due to the faster run and output analysis times required.
Sample Submission:
A sample submission form for needs to be filled out when submitting a sample for Illumina sequencing. You must also download the separate guideline file (Guidelines for completion of Illumina sample submission form). The form should be filled out (light grey boxed sections 1-6), saved under a file name that includes name and date and submitted as soon as possible before delivery/submission of your sample(s). The completed form should be sent by email to: ous-seq@sequencing.uio.no.
The instrument has the following specifics:
- 1 million reads per run
- Single-end or paired-end
- Read lengths ('modal length') 700 bases
- Typical output 700 MB per run
Applications include:
- de novo sequencing of Bacteria, Yeasts, Fungi, Plants, Animals, ...
- sequencing of BACs, Fosmids, Plastids
- resequencing for mutation discovery (SNPs, indels, genomic rearrangements)
- transcriptome analysis (ESTs, SAGE)
- epigenetics (methylation studies)
- metagenomics
- paleogenomics (ancient DNA)
Both whole genome (shotgun/paired-end) and amplicon sequencing (sequencing of PCR products) projects can be performed on the system. The instrument allows for smaller scale projects, as it is possible to combine samples or run smaller analyses, thereby reducing costs.
More than 2000 peer-reviewed papers have been published using this technology.
For a description of some of the applications, refer to the application notes on the 454 website.
Sample Submission:
The 454-Sequencing Submission Form (please read the important information on sheet 2 and 3 in this spreadsheet) should be filled out and submitted as soon as possible before delivery/submission of your sample(s). The completed form should be saved under a file name that includes a name and date, and returned by email to: cees-seq@sequencing.uio.no
Links:
454 sequencing
The instrument has the following specifics:
- Up to 60 000 reads per run
- Read lengths average at 4 500 bases, but 95 percentile is at 11 500 bp and the maximum may exceed 20 000 bp
- Media read error rate ~11% for single pass reads, >99.99% with circular consensus reads
- Total output up to 250 MB per run
Applications include:
- de novo sequencing of Bacteria, Yeasts, Fungi, Plants, Animals, ...
- sequencing of BACs, Fosmids, Plastids
- resequencing for mutation discovery (SNPs, indels, genomic rearrangements)
- transcriptome analysis
- epigenetics (methylation and other base-modifications)
For a description of some of the applications, refer to the application pages on the Pacific Biosciences website.
Sample Submission:
The PacBio-Sequencing Submission Form (please read the important information on sheet 2 and 3 in this spreadsheet) should be filled out and submitted as soon as possible before delivery/submission of your sample(s). The completed form should be saved under a file name that includes a name and date, and returned by email to: cees-seq@sequencing.uio.no
Links:
Pacific Biosciences