Genomics

Photo of the Genomics Team in front of the JCBC

The Genomics facility offers a wide range of services for bulk NGS library preparation, for single cell NGS library preparation, and for spatial transcriptomics.

We prioritise members of the Stem Cell Institute, but the facility is open to academic researchers across Cambridge University, as well as external users from the academic and private sectors.

Bulk projects

Our expertise allows us to produce high quality libraries as well as a reliable and fast turnaround for standard library preparation. We have experience in a wide variety of different library preparation techniques, and we are always happy to try out new things as well.

Range of services

We cater for mainly Transcriptome/RNA sequencing, but have a great deal of experience with other bulk library prep methods:

  • Chip-seq/ Cut&Run
  • ATAC sequencing
  • small RNA sequencing
  • ONT long range sequencing
  • Whole Genome Bisulfite Sequencing
  • Reduced Representation Bisulfite Sequencing
  • Genomic resequencing libraries; and Amplicon sequencing.

Individual projects and non-established methods will always be considered!

Single Cell projects

We regularly process samples using the 10x Genomics Chromium platform. This allows the capture and processing of up to 30,000 single cells per sample for a broad range of Next Generation Sequencing applications including RNA-seq, whole genome sequencing, ATAC-seq or Immune profiling.

Range of single cell services

  • 3’ and 5’ GEM-X
  • Multiome (gene expression and ATAC)
  • VDJ, OCM (On-Chip Multiplexing), FLEX
  • ATAC
  • Cell surface libraries

Interested in any other single cell technology? Please get in touch!

Spatial transcriptomics projects

We are experienced in all 10X Genomics Visium and Xenium sample preparations.

CytAssist enabled Visium HD allows for transcriptome-wide mapping of gene expression onto tissue sections, down to single cell-like level and with associated H&E or IF staining. We can process fresh frozen, fixed frozen or FFPE slides. Localizing a pre-designed panel of proteins in parallel is also possible.

Our team also provides 10x Genomics Xenium services to enable high-plex, high-resolution spatial imaging and analysis, including subcellular RNA detection, high-plex RNA profiling, and spatial tissue mapping. Pre-designed panels and custom panels are available, as well as protein co-detection.

Range of spatial transcriptomics services

  • Visium HD whole transcriptome (mouse or human; probe based)
  • Visium HD 3’ (species agnostic, PolyA based)
  • Xenium v2 assays
  • Xenium 5k assays

Interested in any other spatial transcriptomics technology? Please get in touch!

Services

  • Project planning and advice about your project
  • Advice on any bespoke modifications that might be required for your workflow
  • Advice on choice of sequencing platform
  • RNA/DNA Sample QC
  • Library preparation and QC
  • Pooling of samples and submission to sequencing providers
  • Instrument training for tapestation and bioanalyzer
  • Coordinating workflows and close interaction across facilities such as Histology and Imaging

Sequencing

The sequencing itself is not done in-house, but we have a good working relationship with the CIGC here in Cambridge which allows us access to the latest Illumina sequencing technology. Currently we can offer a wide range of throughput needs on the Novaseq6000.