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Illumina

Contact UsNU-OMICS was one of the first sites in the UK to install the Illumina Miseq in 2013.

We have since built significant experience in small genome sequencing and microbiome studies using Illumina sequencing by synthesis.

Sample preparations are automated using our Hamilton Star liquid handling system. We are not restricted by target for amplicon sequencing. We can help validate new amplicon targets for microbial community sequencing and our academic led facility can support novel approaches or new technologies.  

Please ask if you have a project that is not listed in the application section.

Applications

Bacterial community amplicon sequencing

  • Multiple Amplicon targets
  • 16S rRNA gene sequencing V4 (multiple versions).
  • We have validated studies with other primer targets. Please ask if your target-of-interest could be used for bacterial community projects.

Fungal community amplicon sequencing

  • Multiple Amplicon targets
  • ITS1-2
  • We have validated studies with other primer targets, so please ask if your target-of-interest could be used for fungal community projects.

Small genome sequencing

  • Bacteria
  • Nextera XT
  • Eukaryotic viruses
  • Nextera XT
  • Bacteriophages
  • Nextera XT

Shotgun Metagenomics

  • Untargeted
  • Viral metagenomics DNA and RNA viruses.
  • Methods and bioinformatics designed by academic team.

Bacterial transcriptomics

  • Using ScritpSeq Library Preparation sequencing kit

TruSeq, panel/design for eukaryotic gene expression

Contact for further details or follow the below link to find validated Illumina panels.

https://emea.illumina.com/products/selection-tools/gene-panel-finder.html#/targeted-panels

miRNA sequencing

  • TruSeq Small RNA sequencing

 

 

Sample Requirements Illumina

Please send samples to the following delivery address;

NU-OMICS DNA sequencing research facility
(C/O) Darren Smith/Andrew Nelson
Northumbria University
Ellison Building EBA 504a
Newcastle Upon Tyne
Tyne and Wear
NE1 8ST

Small Genome sequencing; Bacterial or virus

  • NexteraXT
  • All samples must be treated with broad spectrum RNAse prior to sending. An electrophoresis image is required for QA purposes run on a 1% agarose gel. Limited shearing should be present, if worried contact us to check before sending.
  • All samples should be in a 96 well format as parts of the preparation are automated. Data will be returned labelled in well-format over sample name. DNA quality A260/280 should be >1.8.
  • For Nextera XT we require a minimum of 55 ng of DNA in 11ul of elution buffer.

Bacterial and Fungal Community amplicon sequencing

  • DNA sample extraction should be with either phenol:chloroform or for kit based methods we recommend the Qiagen (MoBio) PowerSoil DNA extraction kit.
  • All samples should be in a 96 well format as parts of the preparation are automated. Data will be returned labelled in well-format over sample name. DNA quality A260/280 should be >1.8. Please trial the DNA extraction to see if possible to amplify the target gene in a subset of your samples.
  • Always include a DNA extraction negative. If you use an extraction kit or require multiple kits due to sample numbers please provide a DNA extraction negative for each kit. We will provide a sequencing negative and a commercial mock community so that downstream analysis can be completed (https://www.zymoresearch.eu/zymobiomics-community-standard)

Bacterial RNA sequencing

  • Using ScritpSeq Library Preparation sequencing kit
  • We require a minimum of 1ug of total RNA with RIN value >1.8, although higher is recommended. We can provide QA of total RNA extraction at an extra cost.
  • We are happy to accept libraries already prepared for pooling as long as the supporting QA is available.

Shotgun metagenomics

  • NexteraXT
  • All samples must be treated with broad spectrum RNAse prior to sending. An electrophoresis image is required for QA purposes run on a 1% agarose gel. Limited shearing should be present, if worried email Nuomics@northumbria.ac.uk to check before sending.
  • All samples should be in a 96 well format as parts of the preparation are automated. Data will be returned labelled in well-format over sample name. DNA quality A260/280 should be >1.8.
  • For Nextera XT we require a minimum of 55 ng of DNA in 11ul of elution buffer.

Targeted RNA sequencing from predesigned or bespoke amplicon panels (TruSeq)

  • We require a minimum of 1ug of total RNA with RIN value >1.8, although higher is recommended.
  • We are happy to accept libraries already prepared for pooling as long as the supporting QA is available.

Small RNA sequencing

  • We require a minimum of 1ug of total RNA with RIN value >1.8, although higher is recommended.

Workflow

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