The Genomics Bioinformatics Core (GBC) provides IMS scientists and the wider scientific community, access to state-of-the-art genomics instruments, experimental expertise and bioinformatics services for genomics and transcriptomics studies. We process and analyse more than 1,000 samples with a turnover of >£250K annually and our work is regularly featured in top-tier journals.
Scope:
- Provides scientists of the IMS and wider community access to state-of-the-art genomics instruments, experimental expertise and bioinformatics services for genomics and transcriptomics studies in timely and cost-effective manner.
- Construct sequencing libraries manually or via automation.
- Dedicated 230 TB lustre storage attached directly to our University’s CSD3 High-performance Computing (HPC) cluster at UIS West Cambridge site. Access to popular cloud platforms such as AWS, GCP.
Laboratory facilities
The GBC provides scientific equipment and consumables required for genomics studies, big and small (please see our equipment section for details). We have dedicated pre-PCR and post-PCR rooms for sensitive studies such as ultra-low input, single-cell sequencing.
Next-generation sequencing (NGS) library preparation
We would normally recommend facility users to generate their own NGS libraries under supervision from one of our staff members within the facility, but we are also able to generate libraries at a cost recovery rate.
Bioinformatics and data management
We have setup a dedicated 200TiB lustre storage attached directly to our University’s CSD3 High-performance Computing (HPC) cluster at UIS West Cambridge site. The majority of our work is analysed on the CSD3 cluster which consists of 97,000 CPUs, with 3.5 – 6GiB of memory per CPU. We also have access to popular cloud platforms such as AWS, GCP and DNANexus.
Equipment
| Type of equipment | Details |
|---|---|
| Sequencers | Illumina NovaSeq (via CRUK CIGC) Illumina iSeq100 ABI Sanger Sequencing Service (via Source Bioscience) |
| qPCR Instruments | ABI Quantstudio 5 384-well Analyzer x 2 ABI 7300 96-well Analyzer |
| Sample processing | Beckman Coulter Biomek-i7 Automated Liquid Handler Beckman Coulter Echo 525 Acoustic Liquid Handler Diagenode Bioruptor Pico Sonicator System |
| Single-cell and Spatial Transcriptomics | 10X Genomics Chromium Controller 10X Genomics Chromium iX 10X Genomics CytAssist |
| Sample QC | Agilent Bioanalyzer 2100 Agilent Tapestation 4200 Thermo Nanodrop 2000 |
Key publications
Maki Asami, Brian Y.H. Lam, et al. A program of successive gene expression in mouse one-cell embryos, Cell Reports, 42, 112023 (2023) https://doi.org/10.1016/j.celrep.2023.112023
Steuernagel, L., Lam, B.Y.H., Klemm, P. et al. HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus. Nat Metab 4, 1402–1419 (2022). https://doi.org/10.1038/s42255-022-00657-y
Maki Asami, Brian Y.H. Lam, et al. Human embryonic genome activation initiates at the one-cell stage, Cell Stem Cell, 29, 209-216.e4 (2022) https://doi.org/10.1016/j.stem.2021.11.012.
Lam, B.Y.H., Williamson, A., Finer, S. et al. MC3R links nutritional state to childhood growth and the timing of puberty. Nature 599, 436–441 (2021). https://doi.org/10.1038/s41586-021-04088-9
Bidault G, Virtue S, Petkevicius K, Jolin HE et.al. SREBP1-induced fatty acid synthesis depletes macrophages antioxidant defences to promote their alternative activation. Nat Metab 3, 1150-1162 (2021). https://doi.org/10.1038/s42255-021-00440-5
Wade, K.H., Lam, B.Y.H., Melvin, A. et al. Loss-of-function mutations in the melanocortin 4 receptor in a UK birth cohort. Nat Med 27, 1088–1096 (2021). https://doi.org/10.1038/s41591-021-01349-y
Vacca, M., Leslie, J., Virtue, S. et al. Bone morphogenetic protein 8B promotes the progression of non-alcoholic steatohepatitis. Nat Metab 2, 514–531 (2020). https://doi.org/10.1038/s42255-020-0214-9
