Sequencing

Edinburgh Genomics delivers high-throughput, "next generation" sequencing data from Illumina systems. We also generate Sanger sequence data from AB systems.

 

 

 

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Next Generation Sequencing

The facility operates Illumina HiSeq 2500, HiSeq 4000 and HiSeq X and MiSeq systems as well as the latest PacBio Sequel, and thus has the largest capacity of any University-based sequencing facility in the UK.

Each HiSeq is capable of generating many tens of gigabases per day. These data can be...

  •     assembled de novo to predict the sequence of a new genome or transcriptome
  •     aligned to a reference genome to identify single nucleotide or insertion-deletion polymorphisms
  •     used to count the abundance of species in a DNA mix. The mixes can be the 3' ends of transcripts, small RNAs such as microRNAs or DNA fragments generated by chromatin immunoprecipitation (ChIP) experiments.

We can multiplex several samples per run, so whether you want a "small" number of short reads or hundreds of gigabases, we can deliver.


HiSeq X

The HiSeq X is Illumina's latest population-scale sequencing platform capable of delivering the equivalent of 1,800 human genomes at 30X per instrument per year, producing very high quality data at low cost and fast turnaround times.

The instruments can be used to sequence the genome of any organism at 30X coverage or more across a wide range of genome sizes.

We provide Whole Genome Sequencing (WGS) using our fleet of HiSeq X instruments for small and large projects at competitive prices.

If you are interested in our WGS services, please contact us for futher information.


The Illumina Sequencing Platform

The Illumina sequencing platforms use a small flowcell to immobilise, amplify and sequence up to 1.5 billion molecules at once. HiSeq2500 flowcells come in two flavours:

  • a "rapid" mode, which has two lanes and generates 120-150 million reads or read pairs per lane, up to 150 bases, in 7 to 40 hours

and

  • a "high output mode" which has eight lanes and generates 150-180 million reads or read pairs per lane, up to 100 bases, in 11 days.

MiSeq flowcells currently use a single lane, and can generate up to 20 million reads or read pairs up to 300 bases, in 65 hours.
This flexibility allows the facility to plan runs to suit collaborator needs and to deliver data quickly and efficiently.


The PacBio Sequel

The newly launched PacBio Sequel is based on the RSII proven single molecule, real-time technology with the potential deliver around 7x more reads per SMRT cell.  This platform delivers long reads, high consensus accuracy, uniform coverage and epigenetic characterisation and is ideal for generating high-quality whole genome de novo assemblies. Edinburgh Genomics is proud to be one of the first facilities in the UK to be able to offer this new technology to the sequencing community.  We are validating the system, so get in touch if you want to be part of the early adopter programme.


Sanger Sequencing

The Facility operates an ABI 3730XL capillary sequencing instrument, and can carry out a range of projects from single sequencing reads to medium-scale projects involving tens of thousands of reads (please note, we do not keep any primers for reactions).

We offer...

Analysis of sequenced samples

The user can deliver samples that have already been sequenced with BigDye reagents. We perform clean-up and capillary analysis on the ABI3730XL (any number of samples).

Full sequencing reaction

The user can deliver clean DNA and sequencing primer. We perform the BigDye sequencing, clean-up and capillary analysis on the ABI3730XL (any number of samples).

Larger seqencing projects

The facility is fully equipped to perform larger-scale Sanger sequencing projects. These projects might include expressed sequence tag (EST) surveys, population genetics surveys, sequencing of large insert clones (cosmids, fosmids and BACs), metagenomic surveys, and genome sequencing and resequencing. These projects might typically involve 1000-10000 samples.

Genotyping with microsatellites

We can analyse your PCR-amplified microsatellite or AFLP samples (96 samples at a time) on the ABI3730XL instrument. We can either return the data to you, or assist by giving you access to GeneMapper tools.

Further information:

Sanger sample submission guidelines
Sanger sequencing charges
Sanger sequencing Big Dye reaction
Troubleshooting guide
FAQs

 

Applications

Our sequencing instrumentation is very versatile: if the sample is nucleic acid, we can transform it to a sequencable library. Data generated by Edinburgh Genomics have been applied to questions in a wide range of fields:

 | Genome assembly | SNP discovery | CNV mapping | Genome rearrangements | Genome architecture | Epigenetic modification | Genetic mapping | Quantitative trait genetics | Population genetics | Metagenomics | Metagenetics | Mutation screening | Synthetic biology | Transcriptome assembly | Gene expression | Transcriptional regulation | Phenotyping of mutants | Pathogen discovery | Evolutionary genomics | Host-pathogen interaction | Ecotoxicogenomics |

The Illumina HiSeq X, 4000, 2500 and MiSeq instruments are suited to a wide range of approaches, including

DNASeq

  •     De novo genome sequencing
  •     Genome resequencing
  •     Targeted resequencing
  •     Exome sequencing
  •     Amplicon sequencing
  •     CHIP sequencing (and variants, including 5C)
  •     Methylome sequencing
  •     Genotyping by sequencing
  •     Reduced representation sequencing
  •     Restriction site associated DNA (RAD) sequencing

RNASeq

  •     De novo transcriptome sequencing
  •     Digital transcriptomics
  •     Small RNA sequencing
  •     Total RNA sequencing
  •     Expressed sequence RAD
  •     Stranded RNA sequencing

 

Our technologies

Illumina sequencing produces data at rates orders of magnitude faster than Sanger sequencing, but generates shorter sequences (50 to 300 bases each). Millions to billions of DNA molecules are covalently attached to the surface of a treated glass flowcell, and each individual molecule is amplified in situ to generate a "cluster" that contains about 1000 copies. Sequences are read from newly synthesised DNA copied from these targets by incorporation of fluorescently-tagged nucleotide analogues, illumination with a laser and optical capture of signal from all the amplified clusters simultaneously.

The instruments installed in Edinburgh Genomics are the HiSeq X, 4000, 2500 and the MiSeq.

The HiSeq2500 is a very high volume instrument, generating ~40 billion bases of raw data per day. It uses a flowcell that is about the same size as a large microscope slide, and can capture reads from 35 to 150 bases in length. It can read sequentially from both ends of an immobilised DNA target, generating paired end reads. The HiSeq2500 runs in two modes: "rapid" using a flowcell with two lanes, and producing ~60 Gb of raw data in 36 hrs, or "high output" using a flowcell with eight lanes producing 300 Gb of raw data in ~12 days. Each lane produces up to 200 million reads or read pairs. The HiSeq2500 can run two flowcells at one time. The instrument is mainly used for whole genome sequencing and resequencing (including sequencing of exome or other targeted capture samples), RNA-seq for digital transcriptomics, and sequencing of DNA fragments isolated by immunoprecipitation.

The MiSeq is a benchtop instrument that operates on the same principles as the HiSeq2500, but with further streamlining of the technology that permits longer reads (up to 300 bases) and very rapid run times. It generates ~10 Gb of raw data (or ~20 million reads or read pairs) per run on a pared-down mini-flowcell. The MiSeq is thus ideal for sequencing of smaller genomes (bacteria, fungi, smaller animals and plants), for de novo sequencing of new species' transcriptomes, for bioprospecting ("metabarcoding", pathogen discovery), for smaller scale or pilot experiments, and for technology development. The per-base cost is higher than that of the HiSeq2500.

Our Sanger sequencing install is based on an ABI 3730 instruments This fluorescent capillary sequencer is the workhorse of traditional sequencing, and reliably produce thousands of long (>700 base) high quality reads each day. The technology underpinning fluorescent capillary dideoxy sequencing has been stable for a decade, and we generate from 150,000 to 200,000 reads per year for hundreds of colleagues across the biomedical spectrum. Sequences are read from populations of molecules, sorted by length by a high-resolution capillary electrophoresis, which have been synthesised from a target strand and specifically terminated at each base by the addition of a fluorescently tagged complementary dideoxynucleotide analogue. We can sequence from cloned DNA (as plasmids, fosmids or BACs) or from PCR products.

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