The Genomics Bioinformatics Core (GBC) provides IMS scientists 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.

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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 (especially students and post-docs) to generate their own NGS libraries under supervision from one of our staff members within our 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. 

We have a dedicate team of bioinformaticians who will perform the standard NGS analyses such as sequence alignment, variant calling, gene/exon counting, differential gene expression and pathway analysis.  More bespoke bioinformatics analyses are possible, and charged at a cost-recovery basis. 

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Equipment:

Type of equipment available	Details
Sequencers	Illumina NovaSeq 6000 (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-FXP Automated Liquid Handler 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

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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